(het)aryl-p-quinone derivatives for treatment of mitochondrial diseases

ABSTRACT

Methods of treating or suppressing mitochondrial diseases, such as Friedreich&#39;s ataxia (FRDA), Leber&#39;s Hereditary Optic Neuropathy (LHON), mitochondrial myopathy, encephalopathy, lactacidosis, stroke (MELAS), Kearns-Sayre Syndrome (KSS), are disclosed, as well as compounds useful in the methods of the invention, such as 2-(3-hydroxy-3-methyl-butyl)-6-(het)aryl-p-quinone or as 2-(3-hydroxy-3-methylbutyl)-3-(het)aryl-p-quinone derivatives. Energy biomarkers useful in assessing the metabolic state of a subject and the efficacy of treatment are also disclosed. Methods of modulating, normalizing, or enhancing energy biomarkers, as well as compounds useful for such methods, are also disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority benefit of United States ProvisionalPatent Application No. 61/010,409 filed Jan. 8, 2008, and of U.S.Provisional Patent Application No. 61/010,387 filed Jan. 8, 2008. Bothof those applications are hereby incorporated herein by reference intheir entireties.

TECHNICAL FIELD

The application discloses compositions and methods useful for treatment,prevention, or suppression of diseases, developmental delays andsymptoms related to mitochondrial disorders, such as Friedreich'sataxia, Leber's Hereditary Optic Neuropathy, Kearns-Sayre Syndrome, andmitochondrial myopathy, encephalopathy, lactacidosis, and stroke,cerebral vascular accidents, and for modulating energy biomarkers in asubject. Compositions of the present invention are administered to asubject for the purpose of compensating for mitochondrial dysfunctionand for improving mitochondrial functions. Methods and compounds usefulin treating other disorders such as amyotrophic lateral sclerosis (ALS),Huntington's, Parkinson's and pervasive development disorders are alsodisclosed.

BACKGROUND

Mitochondria are organelles in eukaryotic cells, popularly referred toas the “powerhouse” of the cell. One of their primary functions isoxidative phosphorylation. The molecule adenosine triphosphate (ATP)functions as an energy “currency” or energy carrier in the cell, andeukaryotic cells derive the majority of their ATP from biochemicalprocesses carried out by mitochondria. These biochemical processesinclude the citric acid cycle (the tricarboxylic acid cycle, or Krebscycle), which generates reduced nicotinamide adenine dinucleotide(NADH+H⁺) from oxidized nicotinamide adenine dinucleotide (NAD⁺), andoxidative phosphorylation, during which NADH+H⁺ is oxidized back toNAD⁺. (The citric acid cycle also reduces flavin adenine dinucleotide,or FAD, to FADH₂; FADH₂ also participates in oxidative phosphorylation.)

The electrons released by oxidation of NADH+H⁺ are shuttled down aseries of protein complexes (Complex I, Complex II, Complex III, andComplex IV) known as the mitochondrial respiratory chain. Thesecomplexes are embedded in the inner membrane of the mitochondrion.Complex IV, at the end of the chain, transfers the electrons to oxygen,which is reduced to water. The energy released as these electronstraverse the complexes is used to generate a proton gradient across theinner membrane of the mitochondrion, which creates an electrochemicalpotential across the inner membrane. Another protein complex, Complex V(which is not directly associated with Complexes I, II, III and IV) usesthe energy stored by the electrochemical gradient to convert ADP intoATP.

The citric acid cycle and oxidative phosphorylation are preceded byglycolysis, in which a molecule of glucose is broken down into twomolecules of pyruvate, with net generation of two molecules of ATP permolecule of glucose. The pyruvate molecules then enter the mitochondria,where they are completely oxidized to CO₂ and H₂O via oxidativephosphorylation (the overall process is known as aerobic respiration).The complete oxidation of the two pyruvate molecules to carbon dioxideand water yields about at least 28-29 molecules of ATP, in addition tothe 2 molecules of ATP generated by transforming glucose into twopyruvate molecules. If oxygen is not available, the pyruvate moleculedoes not enter the mitochondria, but rather is converted to lactate, inthe process of anaerobic respiration.

The overall net yield per molecule of glucose is thus approximately atleast 30-31 ATP molecules. ATP is used to power, directly or indirectly,almost every other biochemical reaction in the cell. Thus, the extra(approximately) at least 28 or 29 molecules of ATP contributed byoxidative phosphorylation during aerobic respiration are critical to theproper functioning of the cell. Lack of oxygen prevents aerobicrespiration and will result in eventual death of almost all aerobicorganisms; a few organisms, such as yeast, are able to survive usingeither aerobic or anaerobic respiration.

When cells in an organism are temporarily deprived of oxygen, anaerobicrespiration is utilized until oxygen again becomes available or the celldies. The pyruvate generated during glycolysis is converted to lactateduring anaerobic respiration. The buildup of lactic acid is believed tobe responsible for muscle fatigue during intense periods of activity,when oxygen cannot be supplied to the muscle cells. When oxygen againbecomes available, the lactate is converted back into pyruvate for usein oxidative phosphorylation.

Mitochondrial dysfunction contributes to various disease states. Somemitochondrial diseases are due to mutations or deletions in themitochondrial genome. If a threshold proportion of mitochondria in thecell is defective, and if a threshold proportion of such cells within atissue have defective mitochondria, symptoms of tissue or organdysfunction can result. Practically any tissue can be affected, and alarge variety of symptoms may be present, depending on the extent towhich different tissues are involved.

One such disease is Friedreich's ataxia (FRDA or FA). Friedreich'sataxia is an autosomal recessive neurodegenerative andcardiodegenerative disorder caused by decreased levels of the proteinfrataxin. Frataxin is important for the assembly of iron-sulfur clustersin mitochondrial respiratory-chain complexes. Estimates of theprevalence of FRDA in the United States range from 1 in every22,000-29,000 people (seewww.nlm.nih.gov/medlineplus/ency/article/001411.htm) to 1 in 50,000people (see www.umc-cares.org/health_info/ADAM/Articles/001411.asp). Thedisease causes the progressive loss of voluntary motor coordination(ataxia) and cardiac complications. Symptoms typically begin inchildhood, and the disease progressively worsens as the patient growsolder, patients eventually become wheelchair-bound due to motordisabilities.

Another disease linked to mitochondrial dysfunction is Leber'sHereditary Optic Neuropathy (LHON). The disease is characterized byblindness which occurs on average between 27 and 34 years of age;blindness can develop in both eyes simultaneously, or sequentially (oneeye will develop blindness, followed by the other eye two months lateron average). Other symptoms may also occur, such as cardiacabnormalities and neurological complications.

Yet another syndrome resulting from mitochondrial defects ismitochondrial myopathy, encephalopathy, lactacidosis, and stroke(MELAS). The disease can manifest itself in infants, children, or youngadults. Strokes, accompanied by vomiting and seizures, are one of themost serious symptoms; it is postulated that the metabolic impairment ofmitochondria in certain areas of the brain is responsible for cell deathand neurological lesions, rather than the impairment of blood flow asoccurs in ischemic stroke. Other severe complications, includingneurological symptoms, are often present, and elevated levels of lacticacid in the blood occur.

Yet another syndrome resulting from a respiratory chain disorder isMyoclonus Epilepsy Associated with Ragged-Red Fibers (MERRF) syndrome,one of a group of rare muscular disorders that are called mitochondrialencephalomyopathies. Mitochondrial encephalomyopathies are disorders inwhich a defect in the genetic material arises from a part of the cellstructure that releases energy (mitochondria). This can cause adysfunction of the brain and muscles (encephalomyopathies). Themitochondrial defect as well as “ragged-red fibers” (an abnormality oftissue when viewed under a microscope) are always present. The mostcharacteristic symptom of MERRF syndrome is myoclonic seizures that areusually sudden, brief, jerking, spasms that can affect the limbs or theentire body. Impairment of the ability to coordinate movements (ataxia),as well as an abnormal accumulation of lactic acid in the blood (lacticacidosis) may also be present in affected individuals. Difficultyspeaking (dysarthria), optic atrophy, short stature, hearing loss,dementia, and involuntary jerking of the eyes (nystagmus) may alsooccur.

Yet another syndrome is Leigh's disease, a rare inherited neurometabolicdisorder characterized by degeneration of the central nervous system.Leigh's disease can be caused by mutations in mitochondrial DNA or bydeficiencies of pyruvate dehydrogenase. Symptoms of Leigh's diseaseusually begin between the ages of 3 months to 2 years and progressrapidly. In most children, the first signs may be poor sucking abilityand loss of head control and motor skills. These symptoms may beaccompanied by loss of appetite, vomiting, irritability, continuouscrying, and seizures. As the disorder progresses, symptoms may alsoinclude generalized weakness, lack of muscle tone, and episodes oflactic acidosis, which can lead to impairment of respiratory and kidneyfunction. Heart problems may also occur. In rare cases, Leigh's diseasecan begin during late adolescence or early adulthood and progress moreslowly.

Yet another syndrome resulting from a respiratory chain disorder isCo-Enzyme Q10 Deficiency, the symptoms of which includeencephalomyopathy, mental retardation, exercise intolerance, ragged-redfibers, and recurrent myoglobin in the urine.

Yet another syndrome resulting from a respiratory chain disorder isComplex I Deficiency or NADH dehydrogenase NADH-CoQ reductasedeficiency, the symptoms of which are classified by three major forms:(1) fatal infantile multisystem disorder, characterized by developmentaldelay, muscle weakness, heart disease, congenital lactic acidosis, andrespiratory failure; (2) myopathy beginning in childhood or in adultlife, manifesting as exercise intolerance or weakness; and (3)mitochondrial encephalomyopathy (including MELAS), which may begin inchildhood or adult life and consists of variable combinations ofsymptoms and signs, including ophthalmoplegia, seizures, dementia,ataxia, hearing loss, pigmentary retinopathy, sensory neuropathy, anduncontrollable movements.

Yet another syndrome resulting from a respiratory chain disorder isComplex II Deficiency or Succinate dehydrogenase deficiency, thesymptoms of which include encephalomyopathy and various manifestations,including failure to thrive, developmental delay, hyoptonia, lethargy,respiratory failure, ataxia, myoclonus and lactic acidosis.

Yet another devastating syndrome resulting from a respiratory chaindisorder is Complex II Deficiency or Ubiquinone-cytochrome Coxidoreductase deficiency, symptoms of which are categorized in fourmajor forms: (1) fatal infantile encephalomyopathy, congenital lacticacidosis, hypotonia, dystrophic posturing, seizures, and coma; (2)encephalomyopathies of later onset (childhood to adult life): variouscombinations of weakness, short stature, ataxia, dementia, hearing loss,sensory neuropathy, pigmentary retinopathy, and pyramidal signs; (3)myopathy, with exercise intolerance evolving into fixed weakness; and(4) infantile histiocytoid cardiomyopathy.

Yet another syndrome resulting from a respiratory chain disorder isComplex IV Deficiency or cytochrome C oxidase deficiency, caused by adefect in Complex IV of the respiratory chain, the symptoms of which canbe categorized in two major forms: (1) encephalomyopathy, which istypically normal for the first 6 to 12 months of life and then showdevelopmental regression, ataxia, lactic acidosis, optic atrophy,ophthalmoplegia, nystagmus, dystonia, pyramidal signs, respiratoryproblems and frequent seizures; and (2) myopathy: Two main variants: (a)Fatal infantile myopathy: may begin soon after birth and accompanied byhypotonia, weakness, lactic acidosis, ragged-red fibers, respiratoryfailure, and kidney problems: and (b) Benign infantile myopathy: maybegin soon after birth and accompanied by hypotonia, weakness, lacticacidosis, ragged-red fibers, respiratory problems, but (if the childsurvives) followed by spontaneous improvement.

Yet another syndrome resulting from a respiratory chain disorder isComplex V Deficiency or ATP synthase deficiency includes symptoms suchas slow, progressive myopathy.

Yet another syndrome resulting from a respiratory chain disorder is CPEOor Chronic Progressive External Ophthalmoplegia Syndrome includessymptoms such as visual myopathy, retinitis pigmentosa, or dysfunctionof the central nervous system.

Another mitochondrial disease is Kearns-Sayre Syndrome (KSS). KSS ischaracterized by a triad of features including: (1) typical onset inpersons younger than age 20 years; (2) chronic, progressive, externalophthalmoplegia; and (3) pigmentary degeneration of the retina. Inaddition. KSS may include cardiac conduction defects, cerebellar ataxia,and raised cerebrospinal fluid (CSF) protein levels (e.g., >100 mg/dL).Additional features associated with KSS may include myopathy, dystonia,endocrine abnormalities (e.g., diabetes, growth retardation or shortstature, and hypoparathyroidism), bilateral sensorineural deafness,dementia, cataracts, and proximal renal tubular acidosis. Thus, KSS mayaffect many organ systems.

In addition to congenital disorders involving inherited defectivemitochondria, acquired mitochondrial dysfunction contributes todiseases, particularly neurodegenerative disorders associated with aginglike Parkinson's, Alzheimer's, and Huntington's Diseases. The incidenceof somatic mutations in mitochondrial DNA rises exponentially with age;diminished respiratory chain activity is found universally in agingpeople. Mitochondrial dysfunction is also implicated in excitoxic,neuronal injury, such as that associated with cerebral vascularaccidents, seizures and ischemia.

Recent studies have suggested that as many 20 percent of patients withautism have markers for mitochondrial disease, (Shoffner, J. the 60^(th)Annual American Academy of Neurology meeting in Chicago, Apr. 12-19,2008; Poling, J S et al J. Child Neurol. 2008, 21(2) 170-2; andRossignol et al., Am. J. Biochem. & Biotech. (2008) 4, 208-217.). Somecases of autism have been associated with several different organicconditions, including bioenergetic metabolism deficiency suggested bythe detection of high lactate levels in some patients (Coleman M. et al,Autism and Lactic Acidosis, J. Autism Dev. Disord., (1985) 15: 1-8;Laszlo et al Serum serotonin, lactate and pyruvate levels in infantileautistic children. Clin. Chim. Acta (1994) 229:205-207; and Chugani etal., Evidence of altered energy metabolism in autistic children, Progr.Neuropsychopharmacol. Biol. Psychiat., (1999) 23:635-641) and by nuclearmagnetic resonance imagining as well as positron emission tomographyscanning which documented abnormalities in brain metabolism. Althoughthe mechanism of hyperlactacidemia remains unknown, a likely possibilityinvolves mitochondrial oxidative phosphorylation dysfunction in neuronalcells. A small subset of autistic patients diagnosed with deficienciesin complex I or III of the respiratory chain have been reported in theliterature (see Oliveira, G., Developmental Medicine & Child Neurology(2005) 47 185-189; and Filipek, P A et al., Journal of Autism andDevelopmental Disorders (2004) 34:615-623.) However, in many of thecases of autism where there is some evidence of mitochondrialdysfunction, there is an absence of the classic features associated withmitochondrial disease, such as mitochondrial pathology in muscle biopsy(see Rossignol, D. A. et al., Am J. Biochem. & Biotech, (2008) 4 (2)208-217).

The diseases above appear to be caused by defects in Complex I of therespiratory chain. Electron transfer from Complex I to the remainder ofthe respiratory chain is mediated by the compound coenzyme Q (also knownas Ubiquinone). Oxidized coenzyme Q (CoQ^(ox) or Ubiquinone) is reducedby Complex I to reduced coenzyme Q (CoQ^(red) or Ubiquinol). The reducedcoenzyme Q then transfers its electrons to Complex III of therespiratory chain (skipping over complex II), where it is re-oxidized toCoQ^(ox) (Ubiquinone). CoQ^(ox) can then participate in furtheriterations of electron transfer.

Very few treatments are available for patients suffering from thesediseases. Recently, the compound Idebenone has been proposed fortreatment of Friedreich's ataxia. While the clinical effects ofIdebenone have been relatively modest, the complications ofmitochondrial diseases can be so severe that even marginally usefultherapies are preferable to the untreated course of the disease. Anothercompound, MitoQ, has been proposed for treating mitochondrial disorders(see U.S. Pat. No. 7,179,928); clinical results for MitoQ have not yetbeen reported. For KSS, administration of coenzyme Q10 (CoQ10) andvitamin supplements, have shown only transient beneficial effects inindividual cases.

1,4-Benzoquinones with aryl substitution have been described ininternational patent publication WO 2008/002641 as selective inhibitorsof protein tyrosine phosphatases to treat neoplastic disorders, but thispublication does not specifically disclose2-(3-hydroxy-3-methylbutyl)-6-(het)aryl-p-quinone or2-(3-hydroxy-3-methylbutyl)-3-(het)aryl-p-quinone derivatives, nor theuse of the compounds of this invention for the treatment ofmitochondrial diseases.

The ability to adjust biological production of energy has applicationsbeyond the diseases described above. Various other disorders can resultin suboptimal levels of energy biomarkers (sometimes also referred to asindicators of energetic function), such as ATP levels. Treatments forthese disorders are also needed, in order to modulate one or more energybiomarkers to improve the health of the patient. In other applications,it can be desirable to modulate certain energy biomarkers away fromtheir normal values in an individual that is not suffering from disease.For example, if an individual is undergoing an extremely strenuousundertaking, it can be desirable to raise the level of ATP in thatindividual.

DISCLOSURE OF THE INVENTION

In one embodiment, the invention embraces compounds of Formula I:

-   where,-   R is selected from the group consisting of:

-   where the * indicates the point of attachment of R to the remainder    of the molecule;-   where M and M′ are independently selected from hydrogen, —C(O)—R′,    —C(O)—(C₂-C₆)-alkenyl, —C(O)—(C₂-C₆)-alkynyl, —C(O)-aryl;    —C(O)-heterocyclyl, —C(O)O—R′, —C(O)NR′R″, —SO₂OR′,    —SO₂—(C₁-C₆)-alkyl, —SO₂—(C₁-C₆)-haloalkyl, —SO₂-aryl, —SO₂—NR′R″,    —P(O)(OR′)(OR″), and C-linked mono or di-peptide, where R′ and R″    are independently of each other hydrogen or (C₁-C₆)-alkyl optionally    substituted with —OH, —NH₂, —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂,    —C(O)—OH, —C(O)—O—(C₁-C₄)-alkyl or halogen;-   where either    -   R¹ is aryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-,        wherein the aryl or heterocyclyl is optionally substituted with        one or more substituents selected from (C₁-C₆)-alkyl,        (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl,        hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶,        thiol, (C₁-C₆)-thioalkyl, and —COR⁴; and wherein the        (C₀-C₆)-alkyl group is optionally substituted with OH,        —O(C₁-C₄)-alkyl, —NH₂, —NH(C₁-C₄)-alkyl, —N ((C₁-C₄)-alkyl)₂,        oxo or halogen; and R² and R³ are independently selected from        hydrogen, halogen, (C₁-C₆)-alkyl and (C₁-C₆)-alkoxy;-   or    -   R³ is aryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-,        wherein the aryl or heterocyclyl is optionally substituted with        one or more substituents selected from (C₁-C₆)-alkyl,        (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl-,        hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶,        thiol, (C₁-C₆)-thioalkyl-, and —COR⁴; and wherein the        (C₀-C₆)-alkyl group is optionally substituted with OH,        —O(C₁-C₄)-alkyl, —NH₂, —NH(C₁-C₄)-alkyl, —N ((C₁-C₄)-alkyl)₂,        oxo or halogen; and R¹ and R² are independently selected from        hydrogen, halogen, (C₁-C₆)-alkyl, and (C₁-C₆)-alkoxy;-   where R⁴ is hydrogen, (C₁-C₆)-alkyl, aryl, or aryl-(C₁-C₆)-alkyl-;    and-   where R⁵ and R⁶ are independently of each other hydroxy,    (C₁-C₆)-alkoxy, (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl,    aryl, aryl-(C₁-C₄)-alkyl-, heterocyclyl, or    heterocyclyl-(C₁-C₆)-alkyl-; wherein the alkyl, alkenyl, alkynyl,    aryl and heterocyclyl groups can be further substituted with oxo,    halogen, (C₁-C₆)-haloalkyl, hydroxy, (C₁-C₆)-alkoxy, or —COOR⁴;    or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,    metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount or effective amount of one or more compounds of Formula I asdescribed above.

In another embodiment the invention embraces compounds of Formula Ia ofthe following structure:

-   where either    -   R¹ is aryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-,        wherein the aryl or heterocyclyl is optionally substituted with        one or more substituents selected from (C₁-C₆)-alkyl,        (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl,        hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶,        thiol, (C₁-C₆)-thioalkyl, and —COR⁴; and wherein the        (C₀-C₆)-alkyl group is optionally substituted with OH,        —O(C₁-C₄)-alkyl, —NH₂, —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂, oxo        or halogen; and R² and R³ are independently selected from        hydrogen, halogen, (C₁-C₆)-alkyl and (C₁-C₆)-alkoxy;-   or    -   R³ is aryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-,        wherein the aryl or heterocyclyl is optionally substituted with        one or more substituents selected from (C₁-C₆)-alkyl,        (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl-,        hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶,        thiol, (C₁-C₆)-thioalkyl-, and —COR⁴; and wherein the        (C₀-C₆)-alkyl group is optionally substituted with OH,        —O(C₁-C₄)-alkyl, —NH₂, —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂, oxo        or halogen; and    -   R¹ and R² are independently selected from hydrogen, halogen,        (C₁-C₆)-alkyl, and (C₁-C₆)-alkoxy;-   where R⁴ is hydrogen, (C₁-C₆)-alkyl, aryl, or aryl-(C₁-C₆)-alkyl-;    and-   where R⁵ and R⁶ are independently of each other hydroxy,    (C₁-C₆)-alkoxy, (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl,    aryl, aryl-(C₁-C₆)-alkyl-, heterocyclyl, or    heterocyclyl-(C₁-C₆)-alkyl-; wherein the alkyl, alkenyl, alkynyl,    aryl and heterocyclyl groups can be further substituted with oxo,    halogen, (C₁-C₆)-haloalkyl, hydroxy, (C₁-C₆)-alkoxy, or —COOR⁴;    or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,    metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ib:

-   where,-   R¹ is aryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-, wherein    the aryl or heterocyclyl is optionally substituted with one or more    substituents selected from (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl,    (C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl, hydroxy,    (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, thiol,    (C₁-C₆)-thioalkyl, and —COR⁴; and wherein the (C₀-C₆)-alkyl group is    optionally substituted with OH, —O(C₁-C₄)-alkyl, —NH₂,    —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂, oxo or halogen;-   R² and R³ are independently selected from hydrogen, halogen,    (C₁-C₆)-alkyl, and (C₁-C₆)-alkoxy;-   R⁴ is hydrogen, (C₁-C₆)-alkyl, aryl, or aryl-(C₁-C₆)-alkyl-; and-   R⁵ and R⁶ are independently of each other hydroxy, (C₁-C₆)-alkoxy,    (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, aryl,    aryl-(C₁-C₆)-alkyl-, heterocyclyl, or heterocyclyl-(C₁-C₆)-alkyl-;    wherein the alkyl, alkenyl, alkynyl, aryl, and heterocyclyl groups    can be further substituted with oxo, halogen, (C₁-C₆)-haloalkyl,    hydroxy, (C₁-C₆)-alkoxy, or —COOR⁴;    or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,    metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ib,where R² and R³ are selected from methyl, ethyl, n-propyl, isopropyl,cyclopropyl, n-butyl, isobutyl, sec-butyl, t-butyl, cyclobutyl,cyclopropyl-methyl, methyl-cyclopropyl, pentyl where the point ofattachment of the pentyl group to the remainder of the molecule can beat any location on the pentyl fragment, cyclopentyl, hexyl where thepoint of attachment of the hexyl group to the remainder of the moleculecan be at any location on the hexyl fragment, and cyclohexyl; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ib,where one of the R² and R^(3′) groups is methyl, and the other group ishydrogen. In another embodiment the invention embraces compounds ofFormula Ib, where R² and R³ are methyl; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In another embodiment, the invention embraces compounds of Formula Ib,where one of the R² and R^(3′) groups is methoxy; and in anotherembodiment R² and R^(3′) groups are methoxy.

In another embodiment, the invention embraces compounds of Formula Ib,where one of R² and R³ is halogen, in another embodiment R² and R³ arehalogen, in other embodiments R² and R^(3′) are chloro, bromo, orfluoro.

In another embodiment, the invention embraces compounds of Formula Ib,where R¹ is aryl-(C₀-C₆)-alkyl-, or all salts, stereoisomers, mixturesof stereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.In another embodiment, the invention embraces compounds of Formula Ib,where R¹ is aryl, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof. Inanother embodiment, the invention embraces compounds of Formula Ib,where R¹ is unsubstituted phenyl or naphthyl, or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ib, where R¹ is phenyl or naphthylsubstituted with (C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl, hydroxy,(C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, or —COR⁴; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ib, where R¹ is phenyl substituted withone or more, for example one or two substituents selected from(C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl, hydroxy, (C₁-C₆)-alkoxy, CN,nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, and —COR⁴; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof. In another embodiment, the invention embraces compounds ofFormula Ib, where R¹ is phenyl substituted with one or more substituentsselected from (C₁-C₆)-alkyl, halogen, such as fluoro or chloro, and(C₁₋C₆)-haloalkyl, such as CF₃, or CHF₂; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof. In another embodiment, the invention embraces compounds ofFormula Ib, where R¹ is aryl-(C₁-C₆)alkyl-, optionally substituted withone or more substituents selected from (C₁-C₆)-alkyl, halogen, such asfluoro or chloro, and (C₁-C₆)-haloalkyl, such as CF_or CHF₂; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ib, where R¹ is benzyl, phenylethyl,phenylpropyl, phenylbutyl, phenylpentyl, phenylhexyl, where theattachment of the phenyl to the alkyl chain can be at any open positionand where the phenyl group is optionally substituted with one or moresubstituents selected from (C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl,hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, and —COR⁴;or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof.

In some embodiments, R¹ is phenyl mono-substituted with halogen, such asfluoro or chloro; and in other embodiments. R¹ is phenyl disubstitutedwith halogen such as fluoro or chloro. In another embodiment, R¹ isphenyl substituted with CF₃, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In some embodiments, R¹ is phenyl substituted with hydroxy or(C₁-C₆)-alkoxy; and in some other embodiments R¹ is phenyl substitutedwith methoxy, or all salts, stereoisomers, mixtures of stereoisomers,prodrugs, metabolites, solvates, and hydrates thereof.

In some embodiments, R¹ is phenyl substituted with CN; or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In some embodiments, R¹ is unsubstituted benzyl or unsubstitutedphenylpropyl; or all salts, stereoisomers, mixtures of stereoisomers,prodrugs, metabolites, solvates, and hydrates thereof.

In some embodiments, R¹ is phenyl-(C₁₋₆)-alkyl-, where said alkyl groupis substituted with OH, —O(C₁-C₄)-alkyl, —NH₂, —NH(C₁-C₄)-alkyl,—N((C₁-C₄)-alkyl)₂, oxo or halogen, for example the substituted alkylgroup is 1-hydroxy-2-phenylethyl; or all salts, stereoisomers, mixturesof stereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In some of the prior embodiments, the phenyl substitution is at the paraposition, in other embodiments the phenyl substitution is at the metaposition, and in yet other embodiments the phenyl substitution is at theortho position.

In another embodiment, the invention embraces compounds of Formula Ib,where R¹ is an unsubstituted heterocyclyl-(C₀-C₆)-alkyl-, or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ib, where R¹ is a substitutedheterocyclyl-(C₀-C₆)-alkyl-, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof. Inanother embodiment, the invention embraces compounds of Formula Ib,where R¹ is an optionally substituted nitrogen containing heterocyclyl,for example imidazolyl, pyridinyl, pyrrolyl, and pyrimidinyl, or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ib, where R¹ is an oxygen or sulfurcontaining heterocyclyl, for example tetrahydropyranyl,tetrahydrofuranyl, tetrahydrothienyl, pyranyl, furanyl, thienyl,benzopyranyl, or benzofuranyl, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of the FormulaIc:

-   where,-   R¹ is aryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-, wherein    the aryl or heterocyclyl is optionally substituted with one or more    substituents selected from (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl,    (C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl, hydroxy,    (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, thiol,    (C₁-C₆)-thioalkyl, and —COR⁴; and wherein the (C₀-C₆)-alkyl group is    optionally substituted with OH, —O(C₁-C₆)-alkyl, —NH₂,    —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂, oxo or halogen;-   R² and R³ are independently selected from hydrogen, halogen,    (C₁-C₆)-alkyl, and (C₁-C₆)-alkoxy;-   R⁴ is hydrogen, (C₁-C₆)-alkyl, aryl, or aryl-(C₁-C₆)-alkyl-;-   R⁵ and R⁶ are independently of each other hydroxy, (C₁-C₆)-alkoxy,    (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, aryl,    aryl-(C₁-C₆)-alkyl-, heterocyclyl, or heterocyclyl-(C₁-C₆)-alkyl-;    wherein the alkyl, alkenyl, alkynyl, aryl and heterocyclyl groups    can be further substituted with oxo, halogen, (C₁-C₆)-haloalkyl,    hydroxy, (C₁-C₆)-alkoxy, or —COOR⁴; and-   M and M′ are independently selected from hydrogen, —C(O)—R′,    —C(O)—(C₂-C₆)-alkenyl, —C(O)—(C₂-C₆)-alkynyl, —C(O)-aryl,    —C(O)-heterocyclyl, —C(O)O—R′, —C(O)NR′R″, —SO₂OR′,    —SO₂—(C₁-C₆)-alkyl, —SO₂—(C₁-C₆)-haloalkyl; —SO₂-aryl, —SO₂—NR′R″,    —P(O)(OR′)(OR″), and C-linked mono- or di-peptide, where R′ and R″    are independently of each other hydrogen or (C₁-C₆)-alkyl optionally    substituted with —OH, —NH₂, —NH(C₁-C₄)alkyl, —N((C₁-C₄)alkyl)₂,    —C(O)—OH, —C(O)—O—(C₁-C₄)-alkyl or halogen;    or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,    metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ic,where R² and R³ are selected from methyl, ethyl, n-propyl, isopropyl,cyclopropyl, n-butyl, isobutyl, sec-butyl, i-butyl, cyclobutyl,cyclopropyl-methyl, methyl-cyclopropyl, pentyl where the point ofattachment of the pentyl group to the remainder of the molecule can beat any location on the pentyl fragment, cyclopentyl, hexyl where thepoint of attachment of the hexyl group to the remainder of the moleculecan be at any location on the hexyl fragment and cyclohexyl; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ic,where one of the R² and R³ groups is methyl, and the remaining group ishydrogen. In another embodiment the invention embraces compounds ofFormula Ic, where R² and R³ are methyl; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In another embodiment, the invention embraces compounds of Formula Ic,where one of the R² and R^(3′) groups is methoxy; and in anotherembodiment R² and R^(3′) groups are methoxy.

In another embodiment, the invention embraces compounds of Formula Icwhere one of R² and R³ is halogen, in another embodiment R² and R³ arehalogen, in other embodiments R² and R^(3′) are chloro, bromo, orfluoro.

In another embodiment, the invention embraces compounds of Formula Ic,where R¹ is aryl-(C₀-C₆)-alkyl-, or all salts, stereoisomers, mixturesof stereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.In another embodiment, the invention embraces compounds of Formula Ic,where R¹ is aryl, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof. Inanother embodiment, the invention embraces compounds of Formula Ic,where R¹ is unsubstituted phenyl or unsubstituted naphthyl, or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ic, where R¹ is unsubstituted phenyl, orall salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof. In another embodiment, theinvention embraces compounds of Formula Ic, where R¹ is phenyl ornaphthyl substituted with one or more substituents selected from(C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl, hydroxy, (C₁-C₆)-alkoxy, CN,nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, and —COR⁴; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof. In another embodiment, the invention embraces compounds ofFormula Ic, where R¹ is phenyl substituted with one or two substituentsselected from (C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl, hydroxy,(C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, and —COR⁴; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ic, where R¹ is phenyl substituted withone or more substituents selected from (C₁-C₆)-alkyl, halogen, such asfluoro or chloro, and (C₁-C₆)-haloalkyl, such as CF₃ or CHF₂; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ic, where R¹ is aryl-(C₁-C₆)-alkyl-,substituted with one or more substituents selected from (C₁-C₆)-alkyl,halogen, such as fluoro or chloro, and (C₁-C₆)-haloalkyl, such as CF₃ orCHF₂; or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof. In another embodiment, theinvention embraces compounds of Formula Ic, where R¹ is benzyl,phenylethyl, phenylpropyl, phenylbutyl, phenylpentyl, phenylhexyl, wherethe attachment of the phenyl to the alkyl chain can be at any openposition and where the phenyl group is substituted with one or moresubstituents selected from (C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl,hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, and —COR⁴;or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof.

In some embodiments, R¹ is phenyl mono-substituted with halogen, such asfluoro or chloro, in other embodiments R¹ is phenyl disubstituted withhalogen such as fluoro or chloro. In another embodiment R¹ is phenylsubstituted with CF₃ or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In some embodiments, R¹ is phenyl substituted with hydroxy or(C₁-C₆)-alkoxy; and in some other embodiments R¹ is phenyl substitutedwith methoxy, or all salts, stereoisomers, mixtures of stereoisomers,prodrugs, metabolites, solvates, and hydrates thereof.

In some embodiments, R¹ is phenyl substituted with CN; or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In some embodiments, R¹ is unsubstituted benzyl or unsubstitutedphenylpropyl; or all salts, stereoisomers, mixtures of stereoisomers,prodrugs, metabolites, solvates, and hydrates thereof.

In some of the prior embodiments, the phenyl substitution is at the paraposition, in other embodiments the phenyl substitution is at the metaposition, and in yet other embodiments the phenyl substitution is at theortho position.

In another embodiment, the invention embraces compounds of Formula Ic,where R¹ is an optionally substituted heterocyclyl-(C₀-C₆)-alkyl-, orall salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof. In another embodiment, theinvention embraces compounds of Formula Ic, where R¹ is an optionallysubstituted heterocyclyl, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof. Inanother embodiment, the invention embraces compounds of Formula Ic,where R¹ is a nitrogen containing heterocyclyl, for example imidazolyl,pyridinyl, pyrrolyl, and pyrimidinyl, or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof. In another embodiment, the invention embraces compounds ofFormula Ic, where R¹ is an oxygen or sulfur containing heterocyclyl, forexample tetrahydropyranyl, tetrahydrofuranyl, tetrahydrothienyl,pyranyl, furanyl, thienyl, benzodioxol, benzopyranyl, or benzofuranyl,or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ic,where M and M′ are independently selected from hydrogen and —C(O)—R′; orall salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof. In another embodiment, theinvention embraces compounds of Formula Ic, where M and M′ areindependently selected from hydrogen, —C(O)—H and —C(O)—(C₁-C₆)-alkyl,for example M and M′ are hydrogen or acetyl, or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ic,where R² and R³ are methyl, and M and M′ are hydrogen or acetyl, and asalt, a stereoisomer, or a mixture of stereoisomers. In anotherembodiment, the invention embraces compounds of Formula Ic, where R² andR³ are methyl, R¹ is optionally substituted phenyl, and M and M′ areindependently hydrogen or acetyl, and a salt, a stereoisomer, or amixture of stereoisomers. In another embodiment, the invention embracescompounds of Formula Ic, where R² and R³ are methyl, R¹ is phenyloptionally substituted with one or more, for example one or twohalogens, and M and M′ are independently hydrogen or acetyl, and a salt,a stereoisomer, or a mixture of stereoisomers.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount of one or more compounds of Formula Ib or Formula Ic, where R²and R³ are independently selected from (C₁-C₄) alkyl; and R¹ isoptionally substituted phenyl; or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount of one or more compounds of Formula Ib or Formula Ic, where R²and R³ are methyl; and R¹ is phenyl substituted with one or more, forexample one or two halogens; or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount of one or more compounds of Formula Ic, where M and M′ areindependently selected from hydrogen and acetyl, R² and R³ areindependently selected from (C₁-C₄) alkyl; and R¹ is optionallysubstituted phenyl; or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount or effective amount of one or more compounds of Formula Ic, whereM and M′ are independently selected from hydrogen and acetyl, R² and R³are independently selected from (C₁-C₄) alkyl; and R¹ is phenyloptionally substituted with halogens, or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In another embodiment, the invention embraces compounds of Formula Id:

-   where,-   R¹ and R² are independently selected from hydrogen, halogen,    (C₁-C₆)-alkyl and (C₁-C₆)-alkoxy;-   R³ is aryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-, wherein    the aryl or heterocyclyl is optionally substituted with one or more    substituents selected from (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl,    (C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl-, hydroxy,    (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, thiol,    (C₁-C₆)-thioalkyl-, and —COR⁴; and wherein the (C₀-C₆)-alkyl group    is optionally substituted with OH, —O(C₁-C₄)-alkyl, —NH₂,    —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂, oxo or halogen;-   R⁴ is hydrogen, (C₁-C₆)-alkyl, aryl, or aryl-(C₁-C₆)-alkyl-; and-   R⁵ and R⁶ are independently of each other hydroxy, (C₁-C₆)-alkoxy,    (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, aryl,    aryl-(C₁-C₆)-alkyl-, heterocyclyl, or heterocyclyl-(C₁-C₆)-alkyl-;    wherein the alkyl, alkenyl, alkynyl, aryl, and heterocyclyl groups    can be further substituted with oxo, halogen, (C₁-C₆)-haloalkyl-,    hydroxy, (C₁-C₆)-alkoxy, or —COOR⁴;    or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,    metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Id,where R¹ and R² are selected from methyl, ethyl, n-propyl, isopropyl,cyclopropyl, n-butyl, isobutyl, sec-butyl, t-butyl, cyclobutyl,cyclopropyl-methyl, methyl-cyclopropyl, pentyl where the point ofattachment of the pentyl group to the remainder of the molecule can beat any location on the pentyl fragment, cyclopentyl, hexyl where thepoint of attachment of the hexyl group to the remainder of the moleculecan be at any location on the hexyl fragment, and cyclohexyl; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Id,where one of the R¹ and R^(2′) groups is methyl, and the other group ishydrogen. In another embodiment the invention embraces compounds ofFormula Id, where R¹ and R² are methyl; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In another embodiment, the invention embraces compounds of Formula Id,where one of the R¹ and R^(2′) groups is methoxy; and in anotherembodiment R¹ and R^(2′) groups are methoxy.

In another embodiment, the invention embraces compounds of Formula Id,where one of R¹ and R² is halogen, in another embodiment R¹ and R² arehalogen, in other embodiments R¹ and R^(2′) are chloro, bromo, orfluoro.

In another embodiment, the invention embraces compounds of Formula Id,where R³ is aryl-(C₀-C₆)-alkyl-, or all salts, stereoisomers, mixturesof stereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.In another embodiment, the invention embraces compounds of Formula Id,where R³ is aryl, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof. Inanother embodiment, the invention embraces compounds of Formula Id,where R³ is unsubstituted phenyl or unsubstituted naphthyl, or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Id, where R³ is phenyl or naphthylsubstituted with (C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl-, hydroxy,(C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, or —COR⁴; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Id, where R³ is phenyl substituted withone or more, for example one or two substituents selected from(C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl-, hydroxy, (C₁-C₆)-alkoxy, CN,nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, and —COR⁴; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof. In another embodiment, the invention embraces compounds ofFormula Id, where R³ is phenyl substituted with one or more substituentsselected from C₁-C₆-alkyl, halogen, such as fluoro or chloro, and(C₁-C₆)-haloalkyl-, such as CF₃ or CHF₂; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof. In another embodiment, the invention embraces compounds ofFormula Id, where R³ is aryl-(C₁-C₆) alkyl-, substituted with one ormore substituents selected from (C₁-C₆)-alkyl, halogen, such as fluoroor chloro, and (C₁-C₆)-haloalkyl, such as CF₃ or CHF₂; or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Id, where R³ is benzyl, phenylethyl,phenylpropyl, phenylbutyl, phenylpentyl, phenylhexyl, where theattachment of the phenyl to the alkyl chain can be at any open positionand where the phenyl group is substituted with one or more substituentsselected from (C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl-, hydroxy,(C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, and —COR⁴; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In some embodiments, R³ is phenyl mono-substituted with halogen, such asfluoro or chloro; and in other embodiments. R³ is phenyl disubstitutedwith halogen such as fluoro or chloro. In another embodiment R¹ isphenyl substituted with CF₃, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In some embodiments, R³ is phenyl substituted with hydroxy or(C₁-C₆)-alkoxy; and in some other embodiments R³ is phenyl substitutedwith methoxy, or all salts, stereoisomers, mixtures of stereoisomers,prodrugs, metabolites, solvates, and hydrates thereof.

In some embodiments, R³ is phenyl substituted with CN; or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In some embodiments, R³ is unsubstituted benzyl, unsubstitutedphenylethyl, or unsubstituted phenylpropyl; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In some embodiments, R³ is phenyl-(C₁-C₆)alkyl, where said alkyl groupis substituted with OH, —O(C₁-C₄)-alkyl, —NH₂, —NH(C₁-C₄)-alkyl,—N((C₁-C₄)-alkyl)₂, oxo or halogen, for example when the substitutedalkyl group is 1-hydroxy-2-phenylethyl; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In some of the prior embodiments, the phenyl substitution is at the paraposition, in other embodiments the phenyl substitution is at the metaposition, and in yet other embodiments the phenyl substitution is at theortho position.

In another embodiment, the invention embraces compounds of Formula Id,where R³ is an optionally substituted heterocyclyl-(C₀-C₆)-alkyl-, orall salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof. In another embodiment, theinvention embraces compounds of Formula Id, where R³ is an optionallysubstituted heterocyclyl, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof. Inanother embodiment, the invention embraces compounds of Formula Id,where R³ is an optionally substituted nitrogen containing heterocyclyl,for example imidazolyl, pyridinyl, pyrrolyl, and pyrimidinyl, or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Id, where R³ is an oxygen or sulfurcontaining heterocyclyl, for example tetrahydropyranyl,tetrahydrofuranyl, tetrahydrothienyl, pyranyl, furanyl, thienyl,benzopyranyl, or benzofuranyl, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of the FormulaIe:

-   where,-   R¹ and R² are independently selected from hydrogen, halogen,    (C₁-C₆)-alkyl, and (C₁-C₆)-alkoxy;-   R³ is aryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-, wherein    the aryl or heterocyclyl is optionally substituted with one or more    substituents selected from (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl,    (C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl-, hydroxy,    (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, thiol,    (C₁-C₆)-thioalkyl-, and —COR⁴; and wherein the (C₀-C₆)-alkyl group    is optionally substituted with OH, —O(C₁-C₄)-alkyl, —NH₂,    —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂, oxo or halogen;-   R⁴ is hydrogen, (C₁-C₆)-alkyl, aryl, or aryl-(C₁-C₆)-alkyl-;-   R⁵ and R⁶ are independently of each other hydroxy, (C₁-C₆)-alkoxy,    (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, aryl,    aryl-(C₁-C₆)-alkyl-, heterocyclyl, or heterocyclyl-(C₁-C₆)-alkyl-;    wherein the alkyl, alkenyl, alkynyl, aryl and heterocyclyl groups    can be further substituted with oxo, halogen, (C₁-C₆)-haloalkyl-,    hydroxy, (C₁-C₆)-alkoxy, or —COOR⁴; and-   M and M′ are independently selected from hydrogen, —C(O)—R′,    —C(O)—(C₂-C₆)-alkenyl, —C(O)—(C₂-C₆)-alkynyl, —C(O)-aryl;    —C(O)-heterocyclyl, —C(O)O—R′, —C(O)NR′R″, —SO₂OR′,    —SO₂—(C₁-C₆)-alkyl, —SO₂—(C₁-C₆)-haloalkyl, —SO₂-aryl, —SO₂—NR′R″,    —P(O)(OR′)(OR″), and C-linked mono or di-peptide, where R′ and R″    are independently of each other hydrogen or (C₁-C₆)-alkyl optionally    substituted with —OH, —NH₂, —NH(C₁-C₄)alkyl, —N((C₁-C₄)alkyl)₂,    —C(O)—OH, —C(O)—O—(C₁-C₄)-alkyl or halogen;    or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,    metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ie,where R¹ and R² are selected from methyl, ethyl, n-propyl, isopropyl,cyclopropyl, n-butyl, isobutyl, sec-butyl, t-butyl, cyclobutyl,cyclopropyl-methyl, methyl-cyclopropyl, pentyl where the point ofattachment of the pentyl group to the remainder of the molecule can beat any location on the pentyl fragment, cyclopentyl, hexyl where thepoint of attachment of the hexyl group to the remainder of the moleculecan be at any location on the hexyl fragment and cyclohexyl; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ie,where one of the R¹ and R² groups is methyl, and the remaining group ishydrogen. In another embodiment the invention embraces compounds ofFormula Ie, where R¹ and R², are methyl; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In another embodiment, the invention embraces compounds of Formula Ie,where one of the R¹ and R^(2′) groups is methoxy; and in anotherembodiment R¹ and R² groups are methoxy.

In another embodiment, the invention embraces compounds of Formula Ie,where one of R¹ and R² is halogen, in another embodiment R¹ and R² arehalogen, in other embodiments R¹ and R^(2′) are chloro, bromo, orfluoro.

In another embodiment, the invention embraces compounds of Formula Ie,where R³ is aryl-(C₀-C₆)-alkyl-, or all salts, stereoisomers, mixturesof stereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.In another embodiment, the invention embraces compounds of Formula Ie,where R³ is aryl, or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof. Inanother embodiment, the invention embraces compounds of Formula Ic,where R³ is unsubstituted phenyl or unsubstituted naphthyl, or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ie, where R³ is unsubstituted phenyl, orall salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof. In another embodiment, theinvention embraces compounds of Formula Ie, where R³ is phenyl ornaphthyl substituted with (C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl-,hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, or —COR⁴;or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof. In another embodiment, theinvention embraces compounds of Formula Ie, where R³ is phenylsubstituted with one or more, for example one or two substituentsselected from (C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl-, hydroxy,(C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, and —COR⁴; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ie, where R³ is phenyl substituted withone or more substituents selected from (C₁-C₆)-alkyl, halogen, such asfluoro or chloro, and (C₁-C₆)-haloalkyl-, such as CF₃ or CHF₂; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ie, where R³ is aryl-(C₁-C₆)-alkyl-,substituted with one or more substituents selected from (C₁-C₆)-alkyl,halogen, such as fluoro or chloro, and (C₁-C₆)-haloalkyl, such as CF₃ orCHF₂; or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof. In another embodiment, theinvention embraces compounds of Formula Ie, where R³ is benzyl,phenylethyl, phenylpropyl, phenylbutyl, phenylpentyl, phenylhexyl, wherethe attachment of the phenyl to the alkyl chain can be at any openposition and where the phenyl group is substituted with one or moresubstituents selected from (C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl-,hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, and —COR⁴;or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof.

In some embodiments, R³ is phenyl mono-substituted with halogen, such asfluoro or chloro, in other embodiments R³ is phenyl disubstituted withhalogen such as fluoro or chloro. In another embodiment R³ is phenylsubstituted with CF₃ or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In some embodiments, R³ is phenyl substituted with hydroxy or(C₁-C₆)-alkoxy; and in some other embodiments R³ is phenyl substitutedwith methoxy, or all salts, stereoisomers, mixtures of stereoisomers,prodrugs, metabolites, solvates, and hydrates thereof.

In some embodiments, R³ is phenyl substituted with CN; or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In some embodiments, R³ is phenyl-(C₁-C₆)-alkyl-, or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In some embodiments, R¹ is unsubstitutedbenzyl or unsubstituted phenylpropyl; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In some embodiments, R³ is unsubstituted benzyl or unsubstitutedphenylpropyl; or all salts, stereoisomers, mixtures of stereoisomers,prodrugs, metabolites, solvates, and hydrates thereof.

In some of the prior embodiments, the phenyl substitution is at the paraposition, and in other embodiments the phenyl substitution is at themeta position and in yet other embodiments the phenyl substitution is atthe ortho position.

In another embodiment, the invention embraces compounds of Formula Ie,where R³ is heterocyclyl-(C₀-C₆)-alkyl-, or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof. In another embodiment, the invention embraces compounds ofFormula Ie, where R³ is an optionally substituted heterocyclyl, or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ie, where R³ is a nitrogen containingheterocyclyl, for example imidazolyl, pyrazolyl, pyridinyl, pyrrolyl,pyrimidinyl, pyridazinyl, indolyl, thiazolyl, or oxazolyl, or all salts,stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof. In another embodiment, the inventionembraces compounds of Formula Ie, where R³ is an oxygen or sulfurcontaining heterocyclyl, for example tetrahydropyranyl,tetrahydrofuranyl, tetrahydrothienyl, pyranyl, furanyl, thienyl,benzodioxol, benzopyranyl, or benzofuranyl, or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In another embodiment, the invention embraces compounds of Formula Ic,where M and M′ are independently selected from hydrogen, and —C(O)—R′;or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,metabolites, solvates, and hydrates thereof. In another embodiment, theinvention embraces compounds of Formula Ie, where M and M′ areindependently selected from hydrogen, —C(O)—H and —C(O)—(C₁-C₆)-alkyl,for example M and M′ are independently selected from hydrogen andacetyl, or all salts, stereoisomers, mixtures of stereoisomers,prodrugs, metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula Ie,where R¹ and R² are methyl, and M and M′ are independently selected fromhydrogen and acetyl, and a salt, a stereoisomer, or a mixture ofstereoisomers. In another embodiment, the invention embraces compoundsof Formula Ie, where R¹ and R² are methyl, R³ is optionally substitutedphenyl, and M and M′ are independently selected from hydrogen andacetyl, and a salt, a stereoisomer, or a mixture of stereoisomers. Inanother embodiment, the invention embraces compounds of Formula Ie,where R¹ and R² are methyl, R³ is phenyl optionally substituted with oneor more, for example one or two halogens, and M and M′ are independentlyselected from hydrogen and acetyl, and a salt, a stereoisomer, or amixture of stereoisomers.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount of one or more compounds of Formula Id or Formula Ie, where R¹and R² are independently selected from (C₁-C₄) alkyl; and R isoptionally substituted phenyl; or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount of one or more compounds of Formula Id or Formula Ie, where R¹and R² are independently selected from (C₁-C₄) alkyl; and R¹ is phenylsubstituted with one or more, for example one or two halogens; or allsalts, stereoisomers, mixtures of stereoisomers, prodrugs, metabolites,solvates, and hydrates thereof.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount of one or more compounds of Formula Ie, where M and M′ areindependently selected from hydrogen and acetyl, R¹ and R² areindependently selected from (C₁-C₄) alkyl; and R³ is optionallysubstituted phenyl; or all salts, stereoisomers, mixtures ofstereoisomers, prodrugs, metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount or effective amount of one or more compounds of Formula Ie, whereM and M′ are independently selected from hydrogen and acetyl, R¹ and R²are independently selected from (C₁-C₄) alkyl; and R³ is phenyloptionally substituted with halogens, or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In another embodiment, the invention embraces a method of treating orsuppressing a mitochondrial disorder, modulating one or more energybiomarkers, normalizing one or more energy biomarkers, or enhancing oneor more energy biomarkers, by administering a therapeutically effectiveamount of one or more compounds of Formula I, Formula Ia, Formula Ib,Formula Ic, Formula Id or Formula Ie; or all salts, stereoisomers,mixtures of stereoisomers, prodrugs, metabolites, solvates, and hydratesthereof.

In another embodiment, the invention embraces compounds of Formula I,selected from:

-   2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-6-(4-methoxyphenyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   4-(5-(3-hydroxy-3-methylbutyl)-2,4-dimethyl-3,6-dioxocyclohexa-1,4-dienyl)benzonitrile;-   2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(3,4-difluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-fluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-chlorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;    and-   2-(2,3-dihydrobenzofuran-2-yl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenylcyclohexa-2,5-diene-1,4-dione;-   2-benzyl-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-phenylpropyl)cyclohexa-2,5-diene-1,4-dione;-   2-(1-hydroxy-2-phenylethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-3-(4-methoxyphenyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(4-(trifluoromethyl)-phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(benzofuran-2-yl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-chlorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-ethyl    phenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-(trifluoromethyl)phenyl)-cyclohexa-2,5-diene-1,4-dione;-   2-(4-tert-butylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(4-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   4-(2-(3-hydroxy-3-methylbutyl)-4,5-dimethyl-3,6-dioxocyclohexa-1,4-dienyl)benzonitrile;-   2-(3,4-difluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(2-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-3-(3-methoxyphenyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(4-fluoro-2-methoxyphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(benzo[d][1,3]dioxol-5-yl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(2,4-difluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-3-(4-methoxyphenyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3,5-bis(trifluoromethyl)phenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;    and-   2-(4-chlorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;    or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,    metabolites, solvates, and hydrates thereof.

In another embodiment, the invention embraces compounds of Formula I,selected from:

-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(thiazol-2-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(thiazol-5-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(pyridin-2-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(pyridazin-4-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(thiophen-2-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(thiophen-3-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;-   2-(2-(furan-2-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(2-(furan-3-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(2-(1H-pyrazol-5-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(2-(1H-pyrazol-4-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(2-(1H-pyrazol-1-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(2-(1H-imidazol-5-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(2-(1H-imidazol-2-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(oxazol-5-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(oxazol-2-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(oxazol-4-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;    and-   2-(2-(1H-indol-3-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;    or all salts, stereoisomers, mixtures of stereoisomers, prodrugs,    metabolites, solvates, and hydrates thereof.

In other embodiments, including any of the foregoing embodiments, themitochondrial disorder is selected from the group consisting ofmitochondrial diseases; Myoclonic Epilepsy with Ragged Red Fibers(MERRF); Mitochondrial Myopathy, Encephalopathy, Lactacidosis, andStroke (MELAS); Leber's Hereditary Optic Neuropathy (LHON); chronicprogressive external ophthalmoplegia (CPEO); Leigh Disease; Kearns-SayreSyndrome (KSS); Friedreich's Ataxia (FA); Co-Enzyme Q10 Deficiency;Complex I Deficiency; Complex II Deficiency; Complex III Deficiency;Complex IV Deficiency; Complex V Deficiency; other myopathies;cardiomyopathy; encephalomyopathy; renal tubular acidosis;neurodegenerative diseases; Parkinson's disease; Alzheimer's disease;amyotrophic lateral sclerosis (ALS); motor neuron diseases; otherneurological diseases; epilepsy; genetic diseases; Huntington's Disease;mood disorders; schizophrenia; bipolar disorder; age-associateddiseases; cerebral vascular diseases; macular degeneration; diabetes;pervasive development disorders, such as autistic disorder (ASD),Asperger's disorder, childhood disintegrative disorder (CDD), Rett'sdisorder, and PDD-Not Otherwise Specified (PDD-NOS); and cancer.

In another embodiment, including any of the foregoing embodiments, themitochondrial disorder is a mitochondrial respiratory chain disorder. Ina particular embodiment, the mitochondrial respiratory chain disorder isa respiratory protein chain disorder.

In another embodiment, including any of the foregoing embodiments, themitochondrial disorder is selected from the group consisting ofinherited mitochondrial diseases; Myoclonic Epilepsy with Ragged RedFibers (MERRF); Mitochondrial Myopathy, Encephalopathy, Lactacidosis,and Stroke (MELAS); Leber's Hereditary Optic Neuropathy (LHON); chronicprogressive external ophthalmoplegia (CPEO); Leigh Disease; Kearns-SayreSyndrome (KSS); and Friedreich's Ataxia (FA).

In another embodiment of the invention, including any of the foregoingembodiments, the mitochondrial disorder is Friedreich's ataxia (FRDA).In another embodiment of the invention, the mitochondrial disorder isLeber's Hereditary Optic Neuropathy (LHON). In another embodiment of theinvention, including any of the foregoing embodiments, the mitochondrialdisorder is mitochondrial myopathy, encephalopathy, lactacidosis, andstroke (MELAS). In another embodiment of the invention, including any ofthe foregoing embodiments, the mitochondrial disorder is Kearns-SayreSyndrome (KSS). In another embodiment of the invention, themitochondrial disorder is Myoclonic Epilepsy with Ragged Red Fibers(MERRF). In another embodiment of the invention, including any of theforegoing embodiments, the mitochondrial disorder is Parkinson'sdisease. In another embodiment of the invention, including any of theforegoing embodiments, the mitochondrial disorder is Huntington'sdisease. In another embodiment of the invention, including any of theforegoing embodiments, the mitochondrial disorder is amyotrophic lateralsclerosis disease. In another embodiment, the disorder is cerebralvascular accidents. In another embodiment, the disorder is PervasiveDevelopmental Disorder PDD, including Autistic Disorder (ASD).Asperger's Disorder, Childhood Disintegrative Disorder (CDD), Rett'sDisorder, and PDD-Not Otherwise Specified (PDD-NOS), and in a particularembodiment, the disorder is autism.

In another embodiment of the invention, including any of the foregoingembodiments, the compounds described herein are administered to subjectssuffering from a mitochondrial disorder to modulate one or more ofvarious energy biomarkers, including, but not limited to, lactic acid(lactate) levels, either in whole blood, plasma, cerebrospinal fluid, orcerebral ventricular fluid; pyruvic acid (pyruvate) levels, either inwhole blood, plasma, cerebrospinal fluid, or cerebral ventricular fluid;lactate/pyruvate ratios, either in whole blood, plasma, cerebrospinalfluid, or cerebral ventricular fluid; phosphocreatine levels. NADH(NADH+H⁺) or NADPH (NADPH+H⁺) levels; NAD or NADP levels; ATP levels;reduced coenzyme Q (CoQ^(red)) levels; oxidized coenzyme Q (CoQ^(ox))levels; total coenzyme Q (CoQ^(tot)) levels; oxidized cytochrome Clevels; reduced cytochrome C levels; oxidized cytochrome C/reducedcytochrome C ratio; acetoacetate levels; beta-hydroxy butyrate levels;acetoacetate/beta-hydroxy butyrate ratio; 8-hydroxy-2′-deoxyguanosine(8-OHdG) levels; levels of reactive oxygen species; oxygen consumption(VO2), carbon dioxide output (VCO2), respiratory quotient (VCO2/VO2),and to modulate exercise intolerance (or conversely, modulate exercisetolerance) and to modulate anaerobic threshold. Energy biomarkers can bemeasured in whole blood, plasma, cerebrospinal fluid, cerebroventricularfluid, arterial blood, venous blood, or any other body fluid, body gas,or other biological sample useful for such measurement. In oneembodiment, the levels are modulated to a value within about 2 standarddeviations of the value in a healthy subject. In another embodiment, thelevels are modulated to a value within about 1 standard deviation of thevalue in a healthy subject. In another embodiment, the levels in asubject are changed by at least about 10% above or below the level inthe subject prior to modulation. In another embodiment, the levels arechanged by at least about 20% above or below the level in the subjectprior to modulation. In another embodiment, the levels are changed by atleast about 30% above or below the level in the subject prior tomodulation. In another embodiment, the levels are changed by at leastabout 40% above or below the level in the subject prior to modulation.In another embodiment, the levels are changed by at least about 50%above or below the level in the subject prior to modulation. In anotherembodiment, the levels are changed by at least about 75% above or belowthe level in the subject prior to modulation. In another embodiment, thelevels are changed by at least about 100% above or at least about 90%below the level in the subject prior to modulation.

In another embodiment, including any of the foregoing embodiments, thesubject or subjects in which a method of treating or suppressing amitochondrial disorder, modulating one or more energy biomarkers,normalizing one or more energy biomarkers, or enhancing one or moreenergy biomarkers is performed is/are selected from the group consistingof subjects undergoing strenuous or prolonged physical activity;subjects with chronic energy problems; subjects with chronic respiratoryproblems; pregnant females; pregnant females in labor; neonates;premature neonates; subjects exposed to extreme environments; subjectsexposed to hot environments; subjects exposed to cold environments;subjects exposed to environments with lower-than-average oxygen content;subjects exposed to environments with higher-than-average carbon dioxidecontent; subjects exposed to environments with higher-than-averagelevels of air pollution; airline travelers; flight attendants; subjectsat elevated altitudes; subjects living in cities with lower-than-averageair quality; subjects working in enclosed environments where air qualityis degraded; subjects with lung diseases; subjects withlower-than-average lung capacity; tubercular patients; lung cancerpatients; emphysema patients; cystic fibrosis patients; subjectsrecovering from surgery; subjects recovering from illness; elderlysubjects; elderly subjects experiencing decreased energy; subjectssuffering from chronic fatigue; subjects suffering from chronic fatiguesyndrome; subjects undergoing acute trauma; subjects in shock; subjectsrequiring acute oxygen administration; subjects requiring chronic oxygenadministration; and other subjects with acute, chronic, or ongoingenergy demands who can benefit from enhancement of energy biomarkers.

In another embodiment, the invention embraces one or more compounds ofFormula I, Formula Ia, Formula Ib, Formula Ic, Formula Id and/or FormulaIe, in combination with a pharmaceutically acceptable excipient,carrier, or vehicle.

In another embodiment, the invention embraces the use of one or morecompounds of Formula I, Formula Ia, Formula Ib, Formula Ic, Formula Idand/or Formula Ie, in the therapy of mitochondrial disease. In anotherembodiment, the invention embraces the use of one or more compounds ofFormula I, Formula Ia, Formula Ib, Formula Ic, Formula Id and/or FormulaIe, in the manufacture of a medicament for use in therapy ofmitochondrial disease.

For the purpose of the invention, the compounds of Formula I, FormulaIa, Formula Ib, Formula Ic, Formula Id and/or Formula Ie includederivatives therof wherein one or more hydrogen atoms has been replacedby a hydrogen isotope, for example by deuterium. For the purpose of theinvention, the compounds of Formula I, Formula Ia, Formula Ib, FormulaIc, Formula Id and/or Formula Ie include crystalline form, andnon-crystalline forms therof.

For all of the compounds and methods described above, the quinone formcan also be used in its reduced (hydroquinone) form when desired.Likewise, the hydroquinone form can also be used in its oxidized(quinone) form when desired.

MODES FOR CARRYING OUT THE INVENTION

The invention embraces compounds useful in treating or suppressingmitochondrial disorders, and methods of using such compounds formodulation of energy biomarkers. The redox active therapeutics fortreatment or suppression of mitochondrial diseases and associatedaspects of the invention are described in more detail herein.

By “subject,” “individual,” or “patient” is meant an individualorganism, preferably a vertebrate, more preferably a mammal, mostpreferably a human.

“Treating” a disease with the compounds and methods discussed herein isdefined as administering one or more of the compounds discussed herein,with or without additional therapeutic agents, in order to reduce oreliminate either the disease or one or more symptoms of the disease, orto retard the progression of the disease or of one or more symptoms ofthe disease, or to reduce the severity of the disease or of one or moresymptoms of the disease. “Suppression” of a disease with the compoundsand methods discussed herein is defined as administering one or more ofthe compounds discussed herein, with or without additional therapeuticagents, in order to suppress the clinical manifestation of the disease,or to suppress the manifestation of adverse symptoms of the disease. Thedistinction between treatment and suppression is that treatment occursafter adverse symptoms of the disease are manifest in a subject, whilesuppression occurs before adverse symptoms of the disease are manifestin a subject. Suppression may be partial, substantially total, or total.Because many of the mitochondrial disorders are inherited, geneticscreening can be used to identify patients at risk of the disease. Thecompounds and methods of the invention can then be administered toasymptomatic patients at risk of developing the clinical symptoms of thedisease, in order to suppress the appearance of any adverse symptoms.“Therapeutic use” of the compounds discussed herein is defined as usingone or more of the compounds discussed herein to treat or suppress adisease, as defined above. An “effective amount” of a compound is anamount of the compound sufficient to modulate, normalize, or enhance oneor more energy biomarkers (where modulation, normalization, andenhancement are defined below). A “therapeutically effective amount” ofa compound is an amount of the compound, which, when administered to asubject, is sufficient to reduce or eliminate either a disease or one ormore symptoms of a disease, or to retard the progression of a disease orof one or more symptoms of a disease, or to reduce the severity of adisease or of one or more symptoms of a disease, or to suppress theclinical manifestation of a disease, or to suppress the manifestation ofadverse symptoms of a disease. A therapeutically effective amount can begiven in one or more administrations. An “effective amount” of acompound embraces both a therapeutically effective amount, as well as anamount effective to modulate, normalize, or enhance one or more energybiomarkers in a subject.

By “respiratory chain disorder” is meant a disorder which results in thedecreased utilization of oxygen by a mitochondrion, cell, tissue, orindividual, due to a defect or disorder in a protein contained in themitochondrial respiratory chain. By “respiratory chain” is meant thecomponents (including, but not limited to, proteins, tetrapyrroles, andcytochromes) comprising mitochondrial complex I, II, III, IV, and/or V;“respiratory chain protein” refers to the protein components of thosecomplexes.

“Modulation” of, or to “modulate,” an energy biomarker means to changethe level of the energy biomarker towards a desired value, or to changethe level of the energy biomarker in a desired direction (e.g., increaseor decrease). Modulation can include, but is not limited to,normalization and enhancement as defined below.

“Normalization” of, or to “normalize.” an energy biomarker is defined aschanging the level of the energy biomarker from a pathological valuetowards a normal value, where the normal value of the energy biomarkercan be 1) the level of the energy biomarker in a healthy person orsubject, or 2) a level of the energy biomarker that alleviates one ormore undesirable symptoms in the person or subject. That is, tonormalize an energy biomarker which is depressed in a disease statemeans to increase the level of the energy biomarker towards the normal(healthy) value or towards a value which alleviates an undesirablesymptom; to normalize an energy biomarker which is elevated in a diseasestate means to decrease the level of the energy biomarker towards thenormal (healthy) value or towards a value which alleviates anundesirable symptom.

“Enhancement” of, or to “enhance,” energy biomarkers means tointentionally change the level of one or more energy biomarkers awayfrom either the normal value, or the value before enhancement, in orderto achieve a beneficial or desired effect. For example, in a situationwhere significant energy demands are placed on a subject, it may bedesirable to increase the level of ATP in that subject to a level abovethe normal level of ATP in that subject. Enhancement can also be ofbeneficial effect in a subject suffering from a disease or pathologysuch as a mitochondrial disease, in that normalizing an energy biomarkermay not achieve the optimum outcome for the subject; in such cases,enhancement of one or more energy biomarkers can be beneficial, forexample, higher-than-normal levels of ATP, or lower-than-normal levelsof lactic acid (lactate) can be beneficial to such a subject.

By modulating, normalizing, or enhancing the energy biomarker Coenzyme Qis meant modulating, normalizing, or enhancing the variant or variantsof Coenzyme Q which is predominant in the species of interest. Forexample, the variant of Coenzyme Q which predominates in humans isCoenzyme Q10. If a species or subject has more than one variant ofCoenzyme Q present in significant amounts (i.e., present in amountswhich, when modulated, normalized, or enhanced, can have a beneficialeffect on the species or subject), modulating, normalizing, or enhancingCoenzyme Q can refer to modulating, normalizing or enhancing any or allvariants of Coenzyme Q present in the species or subject.

While the compounds described herein can occur and can be used as theneutral (non-salt) compound, the description is intended to embrace allsalts of the compounds described herein, as well as methods of usingsuch salts of the compounds. In one embodiment, the salts of thecompounds comprise pharmaceutically acceptable salts. Pharmaceuticallyacceptable salts are those salts which can be administered as drugs orpharmaceuticals to humans and/or animals and which, upon administration,retain at least some of the biological activity of the free compound(neutral compound or non-salt compound). The desired salt of a basiccompound may be prepared by methods known to those of skill in the artby treating the compound with an acid. Examples of inorganic acidsinclude, but are not limited to, hydrochloric acid, hydrobromic acid,sulfuric acid, nitric acid, and phosphoric acid. Examples of organicacids include, but are not limited to, formic acid, acetic acid,propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid,malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid,benzoic acid, cinnamic acid, mandelic acid, sulfonic acids, andsalicylic acid. Salts of basic compounds with amino acids, such asaspartate salts and glutamate salts, can also be prepared. The desiredsalt of an acidic compound can be prepared by methods known to those ofskill in the art by treating the compound with a base. Examples ofinorganic salts of acid compounds include, but are not limited to,alkali metal and alkaline earth salts, such as sodium salts, potassiumsalts, magnesium salts, and calcium salts; ammonium salts; and aluminumsalts. Examples of organic salts of acid compounds include, but are notlimited to, procaine, dibenzylamine, N-ethylpiperidine,N,N-dibenzylethylenediamine, and triethylamine salts. Salts of acidiccompounds with amino acids, such as lysine salts, can also be prepared.

The invention also includes all stereoisomers of the compounds,including diasteromers and enantiomers. The invention also includesmixtures of stereoisomers in any ratio, including, but not limited to,racemic mixtures. Unless stereochemistry is explicitly indicated in astructure, the structure is intended to embrace all possiblestereoisomers of the compound depicted. If stereochemistry is explicitlyindicated for one portion or portions of a molecule, but not for anotherportion or portions of a molecule, the structure is intended to embraceall possible stereoisomers for the portion or portions wherestereochemistry is not explicitly indicated.

The compounds can be administered in prodrug form. Prodrugs arederivatives of the compounds which are themselves relatively inactive,but which convert into the active compound when introduced into thesubject in which they are used, by a chemical or biological process invivo, such as an enzymatic conversion. Suitable prodrug formulationsinclude, but are not limited to, peptide conjugates of the compounds ofthe invention and esters of compounds of the inventions. Furtherdiscussion of suitable prodrugs is provided in H. Bundgaard, Design ofProdrugs, New York: Elsevier, 1985; in R. Silverman, The OrganicChemistry of Drug Design and Drug Action, Boston: Elsevier, 2004; in R.L. Juliano (ed.), Biological Approaches to the Controlled Delivery ofDrugs (Annals of the New York Academy of Sciences, v. 507), New York:New York Academy of Sciences, 1987; and in E. B. Roche (ed.), Design ofBiopharmaceutical Properties Through Prodrugs and Analogs (Symposiumsponsored by Medicinal Chemistry Section, APhA Academy of PharmaceuticalSciences, November 1976 national meeting, Orlando, Fla.). Washington:The Academy, 1977.

Metabolites of the compounds are also embraced by the invention.

“(C₁-C₆)-alkyl” is intended to embrace a saturated linear, branched,cyclic, or a combination of linear and/or branched and/or cyclichydrocarbon chain and/or ring of 1 to 6 carbon atoms. Examples of“(C₁-C₆)-alkyl” are methyl, ethyl, n-propyl, isopropyl, cyclopropyl,n-butyl, isobutyl, sec-butyl, t-butyl, cyclobutyl, cyclopropyl-methyl,methyl-cyclopropyl, pentyl where the point of attachment of the pentylgroup to the remainder of the molecule can be at any location on thepentyl fragment, cyclopentyl, hexyl where the point of attachment of thehexyl group to the remainder of the molecule can be at any location onthe hexyl fragment, and cyclohexyl. This term includes mono and divalenthydrocarbon chains, i.e. (C₁-C₆)-alkyl and (C₁-C₆)-alkylene chains of 1to 6 carbon atoms.

“(C₀-C₆)-alkyl” is intended to embrace a saturated linear, branched,cyclic, or a combination of linear and/or branched and/or cyclichydrocarbon chain and/or ring of 1 to 6 carbon atoms, as described abovefor (C₁-C₆)-alkyl, or where the alkyl group is absent. This termincludes mono and divalent hydrocarbon chains, i.e. (C₁-C₆)-alkyl and(C₁-C₆)-alkylene chains of 1 to 6 carbon atoms.

“Halogen” or “halo” designates fluoro (—F), chloro (—Cl), bromo (—Br),and iodo (—I).

“(C₁-C₆)-haloalkyl” is intended to embrace any (C₁-C₆)-alkyl substituenthaving at least one halogen substituent; the halogen can be attached viaany valence on the (C₁-C₆)-alkyl group. One subset of (C₁-C₆)-haloalkylis —CF₃, —CCl₃, —CBr₃, and —CI₃. Another subset of (C₁-C₆)-haloalkyl is—CHF₂, —CHCl₂, —CHBr₂, and —CHI₂. Another subset of (C₁-C₆)-haloalkyl is—CH₂F, —CH₂Cl, —CH₂Br, and —CH₂I. Another subset of (C₁-C₆)-haloalkyl isthe subset of (C₁-C₆)-perhaloalkyls where all available valences arereplaced by halogens. Another subset of (C₁-C₆)-haloalkyl is the subsetof (C₁-C₆)-perfluoroalkyl; where all available valences are replaced byfluorines. Another subset of (C₁-C₆)-haloalkyl is the subset of(C₁-C₆)-perchloroalkyl; that is, (C₁-C₆)-alkyl with all availablevalences replaced by chlorines.

The term “aryl” is intended to embrace an aromatic cyclic hydrocarbongroup of from 6 to 20 carbon atoms having a single ring (e.g., phenyl)or multiple condensed (fused) rings (e.g., naphthyl or anthryl).

The term “Friedreich's ataxia” is intended to embrace other ataxias, andis also sometimes referred to as hereditary ataxia, familiar ataxia, orFriedreich's tabes.

The terms “heterocycle”, “heterocyclic”, “heterocyclo”, and“heterocyclyl” is intended to encompass a monovalent, saturated,partially unsaturated, or unsaturated (heteroaryl) carbocyclic radicalhaving one or more rings incorporating one, two, three or fourheteroatoms within the ring (chosen from nitrogen, oxygen, and/orsulfur). Examples of heterocycles include morpholine, piperidine,piperazine, thiazolidine, pyrazolidine, pyrazoline, imidazolidine,pyrrolidine, tetrahydropyran, tetrahydrofuran, quinuclidine, pyridine,pyrazine, imidazoline, thiazole, isothiazole, pyrazine, triazine,pyrimidine, pyridazine, pyrazole, thiophene, pyrrole, pyran, furan,indole, quinoline, quinazoline, benzodioxole, benzimidazole,benzothiophene, benzofuran, benzoxazole, benzothiazole, benzotriazole,imidazo-pyridines, pyrazolo-pyridines, pyrazolo-pyrazine, acridine,carbazole, and the like.

The terms “Parkinson's”, (also called “Parkinsonism” and “Parkinsoniansyndrome”) (“PD”) is intended to include not only Parkinson's diseasebut also drug-induced Parkinsonism and post-encephalitic Parkinsonism.Parkinson's disease is also known as paralysis agitans or shaking palsy.It is characterized by tremor, muscular rigidity and loss of posturalreflexes. The disease usually progresses slowly with intervals of 10 to20 years elapsing before the symptoms cause incapacity. Due to theirmimicry of effects of Parkinson's disease, treatment of animals withmethamphetamine or MPTP has been used to generate models for Parkinson'sdisease. These animal models have been used to evaluate the efficacy ofvarious therapies for Parkinson's disease.

The term “Pervasive Developmental Disorder” (PDD) is intended to includeneurological disorders characterized by severe and pervasive impairmentin several areas of development, including social interaction andcommunications skills. The five disorders under PDD are AutisticDisorder, Asperger's Disorder, Childhood Disintegrative Disorder (CDD),Rett's Disorder, and PDD-Not Otherwise Specified (PDD-NOS). Specificdiagnostic criteria for each of these disorders can be found in theDiagnostic & Statistical Manual of Mental Disorders (DSM-IV-TR) asdistributed by the American Psychiatric Association (APA). AutisticSpectrum Disorder (ASD) is an umbrella term that is used to represent abroad heterogeneous disorder by collectively grouping autistic disorder,Asperger's Disorder and PDD-NOS.

In general, the nomenclature used in this Application was generated withthe help of naming package within the ChemOffice® version 11.0 suite ofprograms by CambridgeSoft Corp (Cambridge, Mass.).

Diseases Amenable to Treatment or Suppression with Compounds and Methodsof the Invention

A variety of diseases are believed to be caused or aggravated bymitochondrial disorders and impaired energy processing, and can betreated or suppressed using the compounds and methods of the invention.Such diseases include, but are not limited to, inherited mitochondrialdiseases, such as Myoclonic Epilepsy with Ragged Red Fibers (MERRF),Mitochondrial Myopathy, Encephalopathy, Lactacidosis, Stroke (MELAS),Leber's Hereditary Optic Neuropathy (LHON, also referred to as Leber'sDisease, Leber's Optic Atrophy (LOA), or Leber's Optic Neuropathy(LON)), Leigh Disease or Leigh Syndrome, Kearns-Sayre Syndrome (KSS),Friedreich's Ataxia (FA), other myopathies (including cardiomyopathy andencephalomyopathy), and renal tubular acidosis; neurodegenerativediseases, such as Parkinson's disease, Alzheimer's disease, amyotrophiclateral sclerosis (ALS, also known as Lou Gehrig's disease), motorneuron diseases; other neurological diseases such as epilepsy; geneticdiseases such as Huntington's Disease (which is also a neurologicaldisease); mood disorders such as schizophrenia and bipolar disorder; andcertain age-associated diseases, particularly diseases for which CoQ10has been proposed for treatment, such as macular degeneration, diabetes,and cancer. Mitochondrial dysfunction is also implicated in excitoxic,neuronal injury, such as that associated with seizures and ischemia.Mitochondrial dysfunction is also implicated in pervasive developmentdisorders such as autistic syndrome disorder (ASD), Asperger's disorder,childhood sisintegrative sisorder (CDD), Rett's sisorder, and PDD-NotOtherwise Specified (PDD-NOS).

Clinical Assessment of Mitochondrial Dysfunction and Efficacy of Therapy

Several readily measurable clinical markers are used to assess themetabolic state of patients with mitochondrial disorders. These markerscan also be used as indicators of the efficacy of a given therapy, asthe level of a marker is moved from the pathological value to thehealthy value. These clinical markers include, but are not limited to,one or more of the previously discussed energy biomarkers, such aslactic acid (lactate) levels, either in whole blood, plasma,cerebrospinal fluid, or cerebral ventricular fluid; pyruvic acid(pyruvate) levels, either in whole blood, plasma, cerebrospinal fluid,or cerebral ventricular fluid; lactate/pyruvate ratios, either in wholeblood, plasma, cerebrospinal fluid, or cerebral ventricular fluid;phosphocreatine levels, NADH (NADH+H⁺) or NADPH (NADPH+H⁺) levels; NADor NADP levels; ATP levels; anaerobic threshold; reduced coenzyme Q(CoQ^(red)) levels; oxidized coenzyme Q (CoQ^(ox)) levels; totalcoenzyme Q (CoQ^(tot)) levels; oxidized cytochrome C levels; reducedcytochrome C levels; oxidized cytochrome C/reduced cytochrome C ratio;acetoacetate levels, β-hydroxy butyrate levels, acetoacetate/β-hydroxybutyrate ratio, 8-hydroxy-2′-deoxyguanosine (8-OHdG) levels; levels ofreactive oxygen species; and levels of oxygen consumption (VO2), levelsof carbon dioxide output (VCO2), and respiratory quotient (VCO2/VO2).Several of these clinical markers are measured routinely in exercisephysiology laboratories, and provide convenient assessments of themetabolic state of a subject. In one embodiment of the invention, thelevel of one or more energy biomarkers in a patient suffering from amitochondrial disease, such as Friedreich's ataxia, Leber's hereditaryoptic neuropathy, MELAS, or KSS, is improved to within two standarddeviations of the average level in a healthy subject. In anotherembodiment of the invention, the level of one or more of these energybiomarkers in a patient suffering from a mitochondrial disease, such asFriedreich's ataxia, Leber's hereditary optic neuropathy, MELAS, or KSSis improved to within one standard deviation of the average level in ahealthy subject. Exercise intolerance can also be used as an indicatorof the efficacy of a given therapy, where an improvement in exercisetolerance (i.e., a decrease in exercise intolerance) indicates efficacyof a given therapy.

Several metabolic biomarkers have already been used to evaluate efficacyof CoQ10, and these metabolic biomarkers can be monitored as energybiomarkers for use in the methods of the current invention. Pyruvate, aproduct of the anaerobic metabolism of glucose, is removed by reductionto lactic acid in an anaerobic setting or by oxidative metabolism, whichis dependent on a functional mitochondrial respiratory chain.Dysfunction of the respiratory chain may lead to inadequate removal oflactate and pyruvate from the circulation and elevated lactate/pyruvateratios are observed in mitochondrial cytopathies (see Scriver C R, Themetabolic and molecular bases of inherited disease, 7th ed., New York:McGraw-Hill, Health Professions Division, 1995; and Munnich et al., J.Inherit. Metab. Dis. 15(4):448-55 (1992)). Blood lactate/pyruvate ratio(Chariot et al., Arch. Pathol. Lab. Med. 118(7):695-7 (1994)) is,therefore, widely used as a noninvasive test for detection ofmitochondrial cytopathies (see again Scriver C R, The metabolic andmolecular bases of inherited disease, 7th ed., New York: McGraw-Hill,Health Professions Division, 1995; and Munnich et al., J. Inherit.Metab. Dis. 15(4):448-55 (1992)) and toxic mitochondrial myopathies((Chariot et al., Arthritis Rheum. 37(4):583-6 (1994)). Changes in theredox state of liver mitochondria can be investigated by measuring thearterial ketone body ratio (acetoacetate/3-hydroxybutyrate: AKBR) (Uedaet al., J. Cardiol. 29(2):95-102 (1997)). Urinary excretion of8-hydroxy-2′-deoxyguanosine (8-OHdG) often has been used as a biomarkerto assess the extent of repair of ROS-induced DNA damage in bothclinical and occupational settings (Erhola et al., FEBS Lett.409(2):287-91 (1997); Honda et al., Leuk. Res. 24(6):461-8 (2000);Pilger et al., Free Radic. Res. 35(3):273-80 (2001); Kim et al. EnvironHealth Perspect 112(6):666-71 (2004)).

Magnetic resonance spectroscopy (MRS) has been useful in the diagnosesof mitochondrial cytopathy by demonstrating elevations in cerebrospinalfluid (CSF) and cortical white matter lactate using proton MRS (1H-MRS)(Kaufmann et al., Neurology 62(8):1297-302 (2004)). Phosphorous MRS(31P-MRS) has been used to demonstrate low levels of corticalphosphocreatine (PCr) (Matthews et al., Ann. Neurol. 29(4):435-8(1991)), and a delay in PCr recovery kinetics following exercise inskeletal muscle (Matthews et al., Ann. Neurol. 29(4):435-8 (1991);Barbiroli et al., J. Neurol. 242(7):472-7 (1995); Fabrizi et al., J.Neurol. Sci. 137(1):20-7 (1996)). A low skeletal muscle PCr has alsobeen confirmed in patients with mitochondrial cytopathy by directbiochemical measurements.

Exercise testing is particularly helpful as an evaluation and screeningtool in mitochondrial myopathies. One of the hallmark characteristics ofmitochondrial myopathies is a reduction in maximal whole body oxygenconsumption (VO2max) (Taivassalo et al., Brain 126(Pt 2):413-23 (2003)).Given that VO2max is determined by cardiac output (Qc) and peripheraloxygen extraction (arterial-venous total oxygen content) difference,some mitochondrial cytopathies affect cardiac function where deliverycan be altered; however, most mitochondrial myopathies show acharacteristic deficit in peripheral oxygen extraction (A-V O2difference) and an enhanced oxygen delivery (hyperkinetic circulation)(Taivassalo et al., Brain 126(Pt 2):413-23 (2003)). This can bedemonstrated by a lack of exercise induced deoxygenation of venous bloodwith direct AV balance measurements (Taivassalo et al., Ann. Neurol.51(1):38-44 (2002)) and non-invasively by near infrared spectroscopy(Lynch et al., Muscle Nerve 25(5):664-73 (2002); van Beekvelt et al.,Ann. Neurol. 46(4):667-70 (1999)).

Several of these energy biomarkers are discussed in more detail asfollows. It should be emphasized that, while certain energy biomarkersare discussed and enumerated herein, the invention is not limited tomodulation, normalization or enhancement of only these enumerated energybiomarkers.

Lactic Acid (Lactate) Levels:

Mitochondrial dysfunction typically results in abnormal levels of lacticacid, as pyruvate levels increase and pyruvate is converted to lactateto maintain capacity for glycolysis. Mitochondrial dysfunction can alsoresult in abnormal levels of NADH+H⁺, NADPH+H⁺, NAD, or NADP, as thereduced nicotinamide adenine dinucleotides are not efficiently processedby the respiratory chain. Lactate levels can be measured by takingsamples of appropriate bodily fluids such as whole blood, plasma, orcerebrospinal fluid. Using magnetic resonance, lactate levels can bemeasured in virtually any volume of the body desired, such as the brain.

Measurement of cerebral lactic acidosis using magnetic resonance inMELAS patients is described in Kaufmann et al., Neurology 62(8):1297(2004). Values of the levels of lactic acid in the lateral ventricles ofthe brain are presented for two mutations resulting in MELAS, A3243G andA8344G. Whole blood, plasma, and cerebrospinal fluid lactate levels canbe measured by commercially available equipment such as the YSI 2300STAT Plus Glucose & Lactate Analyzer (YSI Life Sciences, Ohio).

NAD, NADP, NADH and NADPH Levels:

Measurement of NAD, NADP, NADH (NADH+H⁺) or NADPH (NADPH+H⁺) can bemeasured by a variety of fluorescent, enzymatic, or electrochemicaltechniques, e.g., the electrochemical assay described in US2005/0067303.

Oxygen Consumption (vO₂ or VO2), Carbon Dioxide Output (vCO₂ or VCO2),and Respiratory Quotient (VCO2/VO2):

vO₂ is usually measured either while resting (resting vO₂) or at maximalexercise intensity (vO₂ max). Optimally, both values will be measured.However, for severely disabled patients, measurement of vO₂ max may beimpractical. Measurement of both forms of vO₂ is readily accomplishedusing standard equipment from a variety of vendors, e.g. Korr MedicalTechnologies, Inc. (Salt Lake City, Utah). VCO2 can also be readilymeasured, and the ratio of VCO2 to VO2 under the same conditions(VCO2/VO2, either resting or at maximal exercise intensity) provides therespiratory quotient (RQ).

Oxidized Cytochrome C, Reduced Cytochrome C, and Ratio of OxidizedCytochrome C to Reduced Cytochrome C:

Cytochrome C parameters, such as oxidized cytochrome C levels (CytC_(ox)), reduced cytochrome C levels (Cyt C_(red)), and the ratio ofoxidized cytochrome C/reduced cytochrome C ratio (Cyt C_(ox))/(CytC_(red)), can be measured by in vivo near infrared spectroscopy. See,e.g., Rolfe, P., “In vivo near-infrared spectroscopy,” Ann. Rev. Biomed.Eng. 2:715-54 (2000) and Strangman et al., “Non-invasive neuroimagingusing near-infrared light” Biol. Psychiatry 52:679-93 (2002).

Exercise Tolerance/Exercise Intolerance:

Exercise intolerance is defined as “the reduced ability to performactivities that involve dynamic movement of large skeletal musclesbecause of symptoms of dyspnea or fatigue” (Piña et al., Circulation107:1210 (2003)). Exercise intolerance is often accompanied bymyoglobinuria, due to breakdown of muscle tissue and subsequentexcretion of muscle myoglobin in the urine. Various measures of exerciseintolerance can be used, such as time spent walking or running on atreadmill before exhaustion, time spent on an exercise bicycle(stationary bicycle) before exhaustion, and the like. Treatment with thecompounds or methods of the invention can result in about a 10% orgreater improvement in exercise tolerance (for example, about a 10% orgreater increase in time to exhaustion, e.g. from 10 minutes to 11minutes), about a 20% or greater improvement in exercise tolerance,about a 30% or greater improvement in exercise tolerance, about a 40% orgreater improvement in exercise tolerance, about a 50% or greaterimprovement in exercise tolerance, about a 75% or greater improvement inexercise tolerance, or about a 100% or greater improvement in exercisetolerance. While exercise tolerance is not, strictly speaking, an energybiomarker, for the purposes of the invention, modulation, normalization,or enhancement of energy biomarkers includes modulation, normalization,or enhancement of exercise tolerance.

Similarly, tests for normal and abnormal values of pyruvic acid(pyruvate) levels, lactate/pyruvate ratio, ATP levels, anaerobicthreshold, reduced coenzyme Q (CoQ^(red)) levels, oxidized coenzyme Q(CoQ^(ox)) levels, total coenzyme Q (CoQ^(tot)) levels, oxidizedcytochrome C levels, reduced cytochrome C levels, oxidized cytochromeC/reduced cytochrome C ratio, acetoacetate levels, β-hydroxy butyratelevels, acetoacetate/β-hydroxy butyrate ratio,8-hydroxy-2′-deoxyguanosine (8-OHdG) levels, and levels of reactiveoxygen species are known in the art and can be used to evaluate efficacyof the compounds and methods of the invention. (For the purposes of theinvention, modulation, normalization, or enhancement of energybiomarkers includes modulation, normalization, or enhancement ofanaerobic threshold.)

Table 1, following, illustrates the effect that various dysfunctions canhave on biochemistry and energy biomarkers. It also indicates thephysical effect (such as a disease symptom or other effect of thedysfunction) typically associated with a given dysfunction. It should benoted that any of the energy biomarkers listed in the table, in additionto energy biomarkers enumerated elsewhere, can also be modulated,enhanced, or normalized by the compounds and methods of the invention.

RQ=respiratory quotient; BMR=basal metabolic rate; HR (CO)=heart rate(cardiac output); T=body temperature (preferably measured as coretemperature); AT=anaerobic threshold; pH=blood pH (venous and/orarterial).

TABLE 1 Site of Measurable, Energy Dysfunction Biochemical EventBiomarker Physical Effect Respiratory ↑ NADH Δ lactate, Metabolic ChainΔ lactate: pyruvate ratio; dyscrasia & and fatigue Δ acetoacetate:β-hydroxy butyrate ratio Respiratory ↓ H⁺ gradient Δ ATP Organ dependentChain dysfunction Respiratory ↓ Electron flux Δ VO₂, RQ, BMR, ΔT,Metabolic Chain AT, pH dyscrasia & fatigue Mitochondria & ↓ ATP, ↓ VO₂ ΔWork, ΔHR (CO) Exercise cytosol intolerance Mitochondria & ↓ ATP Δ PCrExercise cytosol intolerance Respiratory ↓ Cyt C_(Ox/Red) Δ λ~700-900 nM(Near Exercise Chain Infrared Spectroscopy) intolerance Intermediary ↓Catabolism Δ C¹⁴-Labeled substrates Metabolic metabolism dyscrasia &fatigue Respiratory ↓ Electron flux Δ Mixed Venous VO₂ Metabolic Chaindyscrasia & fatigue Mitochondria & ↑ Oxidative stress Δ Tocopherol &Uncertain cytosol Tocotrienols, CoQ10, docosahexanoic acid Mitochondria& ↑ Oxidative stress Δ Glutathione_(red) Uncertain cytosol Mitochondria& Nucleic acid Δ8-hydroxy 2-deoxy Uncertain cytosol oxidation guanosineMitochondria & Lipid oxidation Δ Isoprostane(s), Uncertain cytosoleicasanoids Cell membranes Lipid oxidation Δ Ethane (breath) UncertainCell membranes Lipid oxidation Δ Malondiaidehyde Uncertain

Treatment of a subject afflicted by a mitochondrial disease inaccordance with the methods of the invention may result in theinducement of a reduction or alleviation of symptoms in the subject,e.g., to halt the further progression of the disorder.

Partial or complete suppression of the mitochondrial disease can resultin a lessening of the severity of one or more of the symptoms that thesubject would otherwise experience. For example, partial suppression ofMELAS could result in reduction in the number of stroke-like or seizureepisodes suffered.

Any one or any combination of the energy biomarkers described hereinprovide conveniently measurable benchmarks by which to gauge theeffectiveness of treatment or suppressive therapy. Additionally, otherenergy biomarkers are known to those skilled in the art and can bemonitored to evaluate the efficacy of treatment or suppressive therapy.

Use of Compounds for Modulation of Energy Biomarkers

In addition to monitoring energy biomarkers to assess the status oftreatment or suppression of mitochondrial diseases, the compounds of theinvention can be used in subjects or patients to modulate one or moreenergy biomarkers. Modulation of energy biomarkers can be done tonormalize energy biomarkers in a subject, or to enhance energybiomarkers in a subject.

Normalization of one or more energy biomarkers is defined as eitherrestoring the level of one or more such energy biomarkers to normal ornear-normal levels in a subject whose levels of one or more energybiomarkers show pathological differences from normal levels (i.e.,levels in a healthy subject), or to change the levels of one or moreenergy biomarkers to alleviate pathological symptoms in a subject.Depending on the nature of the energy biomarker, such levels may showmeasured values either above or below a normal value. For example, apathological lactate level is typically higher than the lactate level ina normal (i.e., healthy) person, and a decrease in the level may bedesirable. A pathological ATP level is typically lower than the ATPlevel in a normal (i.e., healthy) person, and an increase in the levelof ATP may be desirable. Accordingly, normalization of energy biomarkerscan involve restoring the level of energy biomarkers to within about atleast two standard deviations of normal in a subject, more preferably towithin about at least one standard deviation of normal in a subject, towithin about at least one-half standard deviation of normal, or towithin about at least one-quarter standard deviation of normal.

Enhancement of the level of one or more energy biomarkers is defined aschanging the extant levels of one or more energy biomarkers in a subjectto a level which provides beneficial or desired effects for the subject.For example, a person undergoing strenuous effort or prolonged vigorousphysical activity, such as mountain climbing, could benefit fromincreased ATP levels or decreased lactate levels. As described above,normalization of energy biomarkers may not achieve the optimum state fora subject with a mitochondrial disease, and such subjects can alsobenefit from enhancement of energy biomarkers. Examples of subjects whocould benefit from enhanced levels of one or more energy biomarkersinclude, but are not limited to, subjects undergoing strenuous orprolonged physical activity, subjects with chronic energy problems, orsubjects with chronic respiratory problems. Such subjects include, butare not limited to, pregnant females, particularly pregnant females inlabor; neonates, particularly premature neonates; subjects exposed toextreme environments, such as hot environments (temperatures routinelyexceeding about 85-86 degrees Fahrenheit or about 30 degrees Celsius forabout 4 hours daily or more), cold environments (temperatures routinelybelow about 32 degrees Fahrenheit or about 0 degrees Celsius for about 4hours daily or more), or environments with lower-than-average oxygencontent, higher-than-average carbon dioxide content, orhigher-than-average levels of air pollution (airline travelers, flightattendants, subjects at elevated altitudes, subjects living in citieswith lower-than-average air quality, subjects working in enclosedenvironments where air quality is degraded); subjects with lung diseasesor lower-than-average lung capacity, such as tubercular patients, lungcancer patients, emphysema patients, and cystic fibrosis patients;subjects recovering from surgery or illness; elderly subjects, includingelderly subjects experiencing decreased energy; subjects suffering fromchronic fatigue, including chronic fatigue syndrome; subjects undergoingacute trauma; subjects in shock; subjects requiring acute oxygenadministration; subjects requiring chronic oxygen administration; orother subjects with acute, chronic, or ongoing energy demands who canbenefit from enhancement of energy biomarkers.

Accordingly, when an increase in a level of one or more energybiomarkers is beneficial to a subject, enhancement of the one or moreenergy biomarkers can involve increasing the level of the respectiveenergy biomarker or energy biomarkers to about at least one-quarterstandard deviation above normal, about at least one-half standarddeviation above normal, about at least one standard deviation abovenormal, or about at least two standard deviations above normal.Alternatively, the level of the one or more energy biomarkers can beincreased by about at least 10% above the subject's level of therespective one or more energy biomarkers before enhancement, by about atleast 20% above the subject's level of the respective one or more energybiomarkers before enhancement, by about at least 30% above the subject'slevel of the respective one or more energy biomarkers beforeenhancement, by about at least 40% above the subject's level of therespective one or more energy biomarkers before enhancement, by about atleast 50% above the subject's level of the respective one or more energybiomarkers before enhancement, by about at least 75% above the subject'slevel of the respective one or more energy biomarkers beforeenhancement, or by about at least 100% above the subject's level of therespective one or more energy biomarkers before enhancement.

When a decrease in a level of one or more energy biomarkers is desiredto enhance one or more energy biomarkers, the level of the one or moreenergy biomarkers can be decreased by an amount of about at leastone-quarter standard deviation of normal in a subject, decreased byabout at least one-half standard deviation of normal in a subject,decreased by about at least one standard deviation of normal in asubject, or decreased by about at least two standard deviations ofnormal in a subject. Alternatively, the level of the one or more energybiomarkers can be decreased by about at least 10% below the subject'slevel of the respective one or more energy biomarkers beforeenhancement, by about at least 20% below the subject's level of therespective one or more energy biomarkers before enhancement, by about atleast 30% below the subject's level of the respective one or more energybiomarkers before enhancement, by about at least 40% below the subject'slevel of the respective one or more energy biomarkers beforeenhancement, by about at least 50% below the subject's level of therespective one or more energy biomarkers before enhancement, by about atleast 75% below the subject's level of the respective one or more energybiomarkers before enhancement, or by about at least 90% below thesubject's level of the respective one or more energy biomarkers beforeenhancement.

Use of Compounds in Research Applications, Experimental Systems, andAssays

The compounds of the invention can also be used in researchapplications. They can be used in vitro, in vivo, or ex vivo experimentsto modulate one or more energy biomarkers in an experimental system.Such experimental systems can be cell samples, tissue samples, cellcomponents or mixtures of cell components, partial organs, whole organs,or organisms. Any one or more of the compounds of Formula I, Formula Ia,Formula Ib, Formula Ic, Formula Id and/or Formula Ie can be used inexperimental systems or research applications. Such researchapplications can include, but are not limited to, use as assay reagents,elucidation of biochemical pathways, or evaluation of the effects ofother agents on the metabolic state of the experimental system in thepresence/absence of one or more compounds of the invention.

Additionally, the compounds of the invention can be used in biochemicaltests or assays. Such tests can include incubation of one or morecompounds of the invention with a tissue or cell sample from a subjectto evaluate a subject's potential response (or the response of aspecific subset of subjects) to administration of said one or morecompounds, or to determine which compound of the invention produces theoptimum effect in a specific subject or subset of subjects. One suchtest or assay would involve 1) obtaining a cell sample or tissue samplefrom a subject in which modulation of one or more energy biomarkers canbe assayed; 2) administering one or more compounds of the invention tothe cell sample or tissue sample; and 3) determining the amount ofmodulation of the one or more energy biomarkers after administration ofthe one or more compounds, compared to the status of the energybiomarker prior to administration of the one or more compounds. Anothersuch test or assay would involve 1) obtaining a cell sample or tissuesample from a subject in which modulation of one or more energybiomarkers can be assayed; 2) administering at least two compounds ofthe invention to the cell sample or tissue sample; 3) determining theamount of modulation of the one or more energy biomarkers afteradministration of the at least two compounds, compared to the status ofthe energy biomarker prior to administration of the at least compounds,and 4) selecting a compound for use in treatment, suppression, ormodulation based on the amount of modulation determined in step 3).

Pharmaceutical Formulations

The compounds described herein can be formulated as pharmaceuticalcompositions by formulation with additives such as pharmaceuticallyacceptable excipients, pharmaceutically acceptable carriers, andpharmaceutically acceptable vehicles. Suitable pharmaceuticallyacceptable excipients, carriers and vehicles include processing agentsand drug delivery modifiers and enhancers, such as, for example, calciumphosphate, magnesium stearate, talc, monosaccharides, disaccharides,starch, gelatin, cellulose, methyl cellulose, sodium carboxymethylcellulose, dextrose, hydroxypropyl-β-cyclodextrin,polyvinylpyrrolidinone, low melting waxes, ion exchange resins, and thelike, as well as combinations of any two or more thereof. Other suitablepharmaceutically acceptable excipients are described in “Remington'sPharmaceutical Sciences,” Mack Pub. Co., New Jersey (1991), and“Remington: The Science and Practice of Pharmacy,” Lippincott Williams &Wilkins. Philadelphia, 20th edition (2003) and 21st edition (2005),incorporated herein by reference.

A pharmaceutical composition can comprise a unit dose formulation, wherethe unit dose is a dose sufficient to have a therapeutic or suppressiveeffect or an amount effective to modulate, normalize, or enhance anenergy biomarker. The unit dose may be sufficient as a single dose tohave a therapeutic or suppressive effect or an amount effective tomodulate, normalize, or enhance an energy biomarker. Alternatively, theunit dose may be a dose administered periodically in a course oftreatment or suppression of a disorder, or to modulate, normalize, orenhance an energy biomarker.

Pharmaceutical compositions containing the compounds of the inventionmay be in any form suitable for the intended method of administration,including, for example, a solution, a suspension, or an emulsion. Liquidcarriers are typically used in preparing solutions, suspensions, andemulsions. Liquid carriers contemplated for use in the practice of thepresent invention include, for example, water, saline, pharmaceuticallyacceptable organic solvent(s), pharmaceutically acceptable oils or fats,and the like, as well as mixtures of two or more thereof. The liquidcarrier may contain other suitable pharmaceutically acceptable additivessuch as solubilizers, emulsifiers, nutrients, buffers, preservatives,suspending agents, thickening agents, viscosity regulators, stabilizers,and the like. Suitable organic solvents include, for example, monohydricalcohols, such as ethanol, and polyhydric alcohols, such as glycols.Suitable oils include, for example, soybean oil, coconut oil, olive oil,safflower oil, cottonseed oil, and the like. For parenteraladministration, the carrier can also be an oily ester such as ethyloleate, isopropyl myristate, and the like. Compositions of the presentinvention may also be in the form of microparticles, microcapsules,liposomal encapsulates, and the like, as well as combinations of any twoor more thereof.

Time-release or controlled release delivery systems may be used, such asa diffusion controlled matrix system or an erodible system, as describedfor example in: Lee. “Diffusion-Controlled Matrix Systems”, pp. 155-198and Ron and Langer, “Erodible Systems”, pp. 199-224, in “Treatise onControlled Drug Delivery”. A. Kydonieus Ed., Marcel Dekker, Inc., NewYork 1992. The matrix may be, for example, a biodegradable material thatcan degrade spontaneously in situ and in vivo for, example, byhydrolysis or enzymatic cleavage, e.g., by proteases. The deliverysystem may be, for example, a naturally occurring or synthetic polymeror copolymer, for example in the form of a hydrogel. Exemplary polymerswith cleavable linkages include polyesters, polyorthoesters,polyanhydrides, polysaccharides, poly(phosphoesters), polyamides,polyurethanes, poly(imidocarbonates) and poly(phosphazenes).

The compounds of the invention may be administered enterally, orally,parenterally, sublingually, by inhalation (e.g. as mists or sprays),rectally, or topically in dosage unit formulations containingconventional nontoxic pharmaceutically acceptable carriers, adjuvants,and vehicles as desired. For example, suitable modes of administrationinclude oral, subcutaneous, transdermal, transmucosal, iontophoretic,intravenous, intraarterial, intramuscular, intraperitoneal, intranasal(e.g. via nasal mucosa), subdural, rectal, gastrointestinal, and thelike, and directly to a specific or affected organ or tissue. Fordelivery to the central nervous system, spinal and epiduraladministration, or administration to cerebral ventricles, can be used.Topical administration may also involve the use of transdermaladministration such as transdermal patches or iontophoresis devices. Theterm parenteral as used herein includes subcutaneous injections,intravenous, intramuscular, intrasternal injection, or infusiontechniques. The compounds are mixed with pharmaceutically acceptablecarriers, adjuvants, and vehicles appropriate for the desired route ofadministration. Oral administration is a preferred route ofadministration, and formulations suitable for oral administration arepreferred formulations. The compounds described for use herein can beadministered in solid form, in liquid form, in aerosol form, or in theform of tablets, pills, powder mixtures, capsules, granules,injectables, creams, solutions, suppositories, enemas, colonicirrigations, emulsions, dispersions, food premixes, and in othersuitable forms. The compounds can also be administered in liposomeformulations. The compounds can also be administered as prodrugs, wherethe prodrug undergoes transformation in the treated subject to a formwhich is therapeutically effective. Additional methods of administrationare known in the art.

Injectable preparations, for example, sterile injectable aqueous oroleaginous suspensions, may be formulated according to the known artusing suitable dispersing or wetting agents and suspending agents. Thesterile injectable preparation may also be a sterile injectable solutionor suspension in a nontoxic parenterally acceptable diluent or solvent,for example, as a solution in propylene glycol. Among the acceptablevehicles and solvents that may be employed are water, Ringer's solution,and isotonic sodium chloride solution. In addition, sterile, fixed oilsare conventionally employed as a solvent or suspending medium. For thispurpose any bland fixed oil may be employed including synthetic mono- ordi-glycerides. In addition, fatty acids such as oleic acid find use inthe preparation of injectables.

Solid dosage forms for oral administration may include capsules,tablets, pills, powders, and granules. In such solid dosage forms, theactive compound may be admixed with at least one inert diluent such assucrose, lactose, or starch. Such dosage forms may also compriseadditional substances other than inert diluents, e.g., lubricatingagents such as magnesium stearate. In the case of capsules, tablets, andpills, the dosage forms may also comprise buffering agents. Tablets andpills can additionally be prepared with enteric coatings.

Liquid dosage forms for oral administration may include pharmaceuticallyacceptable emulsions, solutions, suspensions, syrups, and elixirscontaining inert diluents commonly used in the art, such as water. Suchcompositions may also comprise adjuvants, such as wetting agents,emulsifying and suspending agents, cyclodextrins, and sweetening,flavoring, and perfuming agents.

The compounds of the present invention can also be administered in theform of liposomes. As is known in the art, liposomes are generallyderived from phospholipids or other lipid substances. Liposomes areformed by mono- or multilamellar hydrated liquid crystals that aredispersed in an aqueous medium. Any non-toxic, physiologicallyacceptable and metabolizable lipid capable of forming liposomes can beused. The present compositions in liposome form can contain, in additionto a compound of the present invention, stabilizers, preservatives,excipients, and the like. The preferred lipids are the phospholipids andphosphatidyl cholines (lecithins), both natural and synthetic. Methodsto form liposomes are known in the art. See, for example, Prescott, Ed.,Methods in Cell Biology, Volume XIV, Academic Press, New York, N.W., p.33 et seq (1976).

The invention also provides articles of manufacture and kits containingmaterials useful for treating or suppressing mitochondrial diseases. Theinvention also provides kits comprising any one or more of the compoundsof Formula I, Formula Ia, Formula Ib, Formula Ic, Formula Id and/orFormula Ie. In some embodiments, the kit of the invention comprises thecontainer described above.

In other aspects, the kits may be used for any of the methods describedherein, including, for example, to treat an individual with amitochondrial disorder, or to suppress a mitochondrial disorder in anindividual.

The amount of active ingredient that may be combined with the carriermaterials to produce a single dosage form will vary depending upon thehost to which the active ingredient is administered and the particularmode of administration. It will be understood, however, that thespecific dose level for any particular patient will depend upon avariety of factors including the activity of the specific compoundemployed, the age, body weight, body area, body mass index (BMI),general health, sex, diet, time of administration, route ofadministration, rate of excretion, drug combination, and the type,progression, and severity of the particular disease undergoing therapy.The pharmaceutical unit dosage chosen is usually fabricated andadministered to provide a defined final concentration of drug in theblood, tissues, organs, or other targeted region of the body. Thetherapeutically effective amount or effective amount for a givensituation can be readily determined by routine experimentation and iswithin the skill and judgment of the ordinary clinician.

Examples of dosages which can be used are an effective amount within thedosage range of about 0.1 mg/kg to about 300 mg/kg body weight, orwithin about 1.0 mg/kg to about 100 mg/kg body weight, or within about1.0 mg/kg to about 50 mg/kg body weight, or within about 1.0 mg/kg toabout 30 mg/kg body weight, or within about 1.0 mg/kg to about 10 mg/kgbody weight, or within about 10 mg/kg to about 100 mg/kg body weight, orwithin about 50 mg/kg to about 150 mg/kg body weight, or within about100 mg/kg to about 200 mg/kg body weight, or within about 150 mg/kg toabout 250 mg/kg body weight, or within about 200 mg/kg to about 300mg/kg body weight, or within about 250 mg/kg to about 300 mg/kg bodyweight. Compounds of the present invention may be administered in asingle daily dose, or the total daily dosage may be administered individed dosage of two, three or four times daily.

While the compounds of the invention can be administered as the soleactive pharmaceutical agent, they can also be used in combination withone or more other agents used in the treatment or suppression ofdisorders. Representative agents useful in combination with thecompounds of the invention for the treatment or suppression ofmitochondrial diseases include, but are not limited to, Coenzyme Q,vitamin E, idebenone, MitoQ, vitamins, and antioxidant compounds.

When additional active agents are used in combination with the compoundsof the present invention, the additional active agents may generally beemployed in therapeutic amounts as indicated in the Physicians' DeskReference (PDR) 53rd Edition (1999), which is incorporated herein byreference or such therapeutically useful amounts as would be known toone of ordinary skill in the art.

The compounds of the invention and the other therapeutically activeagents can be administered at the recommended maximum clinical dosage orat lower doses. Dosage levels of the active compounds in thecompositions of the invention may be varied so as to obtain a desiredtherapeutic response depending on the route of administration, severityof the disease and the response of the patient. When administered incombination with other therapeutic agents, the therapeutic agents can beformulated as separate compositions that are given at the same time ordifferent times, or the therapeutic agents can be given as a singlecomposition.

The invention will be further understood by the following non-limitingexamples.

EXAMPLES Synthesis of Compounds Example 12-(3-Hydroxy-3-methylbutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dioneStep 1: (2,6-Dimethyl-1,4-phenylene)bis(oxy)bis(methylene)dibenzene

To a stirring solution of 2,6 dimethylhydroquinone (5 g, 36.2 mmol) in50 mL dimethoxyethane at 23° C. was added a solution of elementalbromine (1.83 mL, 35.8 mmol) in 40 mL dimethoxyethane, dropwise over 75min. After an additional 15 min, excess bromine was quenched with a 1 Maqueous solution of sodium thiosulfate (25 mL) and the resulting whiteemulsion was diluted in 150 mL EtOAc and 100 mL 1 M aqueous sodiumbicarbonate. The organic layer was washed once with brine, and driedover anhydrous sodium sulfate. The solution was filtered andconcentrated in vacuo to a brown solid. The residue was taken up indimethylformamide (60 mL), and the resulting solution was degassed withArgon for 5 min, after which potassium carbonate (14.5 g, 105 mmol), andbenzyl bromide (9.3 mL, 78 mmol) were added rapidly. The resultingsuspension was stirred for 18 hr at 65° C. after which it was diluted in400 mL methyl tertiary-butyl ether (MTBE), 200 mL hexanes, and 200 mLbrine. The resulting emulsion was broken upon acidification to pH 4 with1 M aqueous citric acid. The organics were removed, washed twice with2.5 M aqueous ammonia, and once with brine (50 mL each). The remainingorganics were dried over anhydrous sodium sulfate, filtered andconcentrated in vacuo. Filtration on a silica gel plug (7%EtOAc/hexanes) yielded 2.8 g yellow solid, which was digested in 25 mLhexanes to produce 2.4 g yellow solid product, which was digested in 10%aqueous ethanol to produce the benzylated compound(2,6-dimethyl-1,4-phenylene)bis(oxy)bis(methylene)dibenzene, 7.7 g. ¹HNMR (CDC₃, 400 MHz) 7.55-7.40 (m, 10H), 6.85 (s, 1H), 5.05 (s, 2H), 4.74(s, 2H), 2.35 (s, 3H), 2.21 (s, 3H) ppm.

Step 2: 2,2,5,7-tetramethyl-8-(4-(trifluoromethyl)phenyl)chroman-6-ol

Into a 20-mL scintillation vial, the following solids were measured:(2,6-dimethyl-1,4-phenylene)bis(oxy)bis(methylene)dibenzene (400 mg,1.01 mmol), 4-trifluoromethylphenylboronic acid (229 mg, 1.21 mmol),dichloro 1,1′-bis(diphenylphosphino)ferrocene palladium (II)dichloromethane adduct (22 mg, 30 μmol), and cesium fluoride (536 mg,3.53 mmol). The solids were taken up in 10) mL ethanol, the flask wassealed, and the resulting mixture stirred at 60° C. After the reactionhad stirred for 18 hr, the mixture was filtered, concentrated in vacuo.The residue was diluted in 50 ml. EtOAc, and washed with 20 mL each of 1M aqueous citric acid and brine. The remaining organics were dried overanhydrous sodium sulfate, filtered and concentrated in vacuo. A crudepurification was performed by filtration of the residue on silica gelplug (0→10% EtOAc/hexanes), yielding 300 mg of white solid thatcontained a mixture of the desired product and several small impurities.The resulting material was dissolved in a THF-ethanol mixture (3.5 mL,1:1), charged with 5% palladium on carbon (73 mg, 35 μmol), andhydrogenated at ambient pressure. After stirring for 4 hr, the blacksuspension was filtered and concentrated in vacuo. The residue wasrapidly dissolved in toluene (8 mL), degassed with Argon for 2 min. thencharged with 2-methyl-3-buten-2-ol (170 μL, 1.6 mmol), and BF₃.OEt₂ (200μL, 1.6 mmol). The resulting brown solution was stirred at 100° C. After45 min, the reaction mixture was washed once with 1 M aqueous sodiumbicarbonate, dried over anhydrous sodium sulfate, filtered andconcentrated in vacuo. Purification by silica gel column chromatography(0→15% EtOAc/hexanes) afforded a yellow oil containing2,2,5,7-tetramethyl-8-(4-(trifluoromethyl)phenyl)chroman-6-ol and someimpurities (160 mg). ¹H NMR (CDCl₃, 400 MHz) 7.6 (d, 2H), 7.3 (d, 2H),4.25 (s, 1H), 2.65 (t, 2H), 2.17 (s, 3H), 1.94 (s, 3H), 1.75 (t, 2H),1.16 (s, 6H) ppm.

Step 3:2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione

The purified residue containing2,2,5,7-tetramethyl-8-(4-(trifluoromethyl)phenyl) chroman-6-ol from theabove reaction (60 mg) was dissolved in THF/acetonitrile (1:1, 2 ml) andcooled in an ice-water bath. To the resulting solution was addeddropwise an aqueous solution of ceric ammonium nitrate (170 mg, 310 μmolin 1 mL) until a reddish color persisted. When the titration endpointwas reached, the mixture was diluted in 5 mL EtOAc, washed once withbrine (2 mL). The remaining organics were dried over anhydrous sodiumsulfate, filtered and concentrated in vacuo. Purification by silica gelcolumn chromatography (5→25% EtOAc/hexanes) producing 80 mg of2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione,a yellow oil. ¹H NMR (CDCl₃, 400 MHz) 7.67 (d, 2H), 7.26 (d, 2H), 2.60(m, 2H), 2.11 (s, 3H), 1.92 (s, 3H), 1.54 (m, 2H), 1.25 (s, 6H) ppm.

Similarly, substituting in Step 2 4-trifluoromethylphenylboronic acidfor other appropriate boronic acids, the following additional compoundswere prepared.

Example 22-(3-Hydroxy-3-methylbutyl)-6-(4-methoxyphenyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.07 (m, 3H), 6.93 (d, 2H), 3.82 (s, 3H), 2.59(m, 2H), 2.09 (s, 3H), 1.96 (s, 3H), 1.55 (m, 2H), 1.25 (s, 6H) ppm.

Example 34-(5-(3-Hydroxy-3-methylbutyl)-2,4-dimethyl-3,6-dioxocyclohexa-1,4-dienyl)benzonitrile

¹H NMR (CDCl₃, 400 MHz) 7.70 (d, 2H), 7.25 (d, 2H), 2.60 (m, 2H), 2.11(s, 3H), 1.92 (s, 3H), 1.53 (m, 2H), 1.26 (s, 6H) ppm.

Example 42-(3-Hydroxy-3-methylbutyl)-3,5-dimethyl-6-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.86 (m, 3H), 7.61 (br s, 1H), 2.49 (m, 2H),2.13 (s, 3H), 1.97 (s, 3H), 1.56 (m, 2H), 1.26 (s, 6H) ppm.

Example 52-(3,4-Difluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.20 (q, 1H), 6.98 (td, 1H), 6.86 (d, 1H), 2.60(m, 2H), 2.10 (s, 3H), 1.94 (s, 3H), 1.53 (m, 2H), 1.26 (s, 6H) ppm.

Example 62-(4Fluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.15 (m, 4H), 2.60 (m, 2H), 2.10 (s, 3H), 1.93(s, 3H), 1.54 (m, 2H), 1.25 (s, 6H) ppm.

Example 72-(4-chlorophenyl)-6-(3-hydroxo-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.40 (d, 2H), 7.09 (d, 2H), 2.62 (t, 2H), 2.11(s, 3H), 1.95 (s, 3H), 1.55 (t, 2H), 1.34 (s, 1H), 1.27 (s, 6H) ppm.

Example 82-(2,3-dihydrobenzofuran-2-yl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.64 (d, 1H), 7.51 (d, 1H), 7.30 (m, 2H), 6.55(s, 1H), 2.64 (t, 2H), 2.37 (s, 3H), 2.08 (s, 3H), 1.57 (t, 2H), 1.37(s, 1H), 1.30 (s, 6H) ppm.

Example 92-(4-Fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dioneStep 1(5-Bromo-2,3-dimethyl-1,4-phenylene)bis(oxy)bis(methylene)dibenzene

To a stirring solution of 2,3-dimethylbenzene-1,4-diol (5 g, 35.1 mmol)in 87.7 mL dimethoxyethane at 23° C. was added elemental bromine (1.83mL, 35.8 mmol) dropwise over 5 min. After an additional 15 min (20 mintotal), excess bromine was quenched with a 1 M aqueous solution ofsodium thiosulfate (25 mL) and the resulting white emulsion was dilutedin 150 mL EtOAc and 100 mL H₂O. The organics were removed and washedtwice with 1 M aqueous sodium bicarbonate, once with brine, and driedover anhydrous sodium sulfate. The solution was filtered andconcentrated in vacuo to a brown solid. The residue was taken up indimethylformamide (58 mL), and the resulting solution was degassed withargon for 5 min, after which potassium carbonate (14.5 g, 105 mmol), andbenzyl bromide (9.3 mL, 78 mmol) were added rapidly. The resultingsuspension was stirred for 18 hr. after which it was diluted in 200 mLEtOAc, 200 mL hexanes, and 200 mL H₂O. The resulting emulsion was brokenupon acidification to pH 4 with 1 M aqueous citric acid. The organicswere removed, then washed twice with H₂O, and once with brine (50 mLeach). The remaining organics were dried over anhydrous sodium sulfate,filtered and concentrated in vacuo. Filtration on a silica gel plug (7%EtOAc/hexanes) yielded 2.8 g of a yellow solid, which was digested in 25mL hexanes to produce 2.33 g of(5-bromo-2,3-dimethyl-1,4-phenylene)bis(oxy)bis(methylene)dibenzene aswhite solid product. ¹H NMR (CDCl₃, 400 MHz) 7.55 (d, 2H), 7.40 (m, 8H),7.0 (s, 1H), 5.00 (s, 2H), 4.80 (s, 2H), 2.21 (s, 3H), 2.15 (s, 31H)ppm.

Step 2 5-(4-fluorophenyl)-2,2,7,8-teramethylchroman-6-ol

Into a 20-mL scintillation vial, the following solids were measured:compound B (400 mg, 1.01 mmol), 4-fluorophenylboronic acid (170 mg, 1.21mmol), dichloro 1,1′-bis(diphenylphosphino) ferrocene palladium (II)dichloromethane adduct (22 mg, 30 μmol), and cesium fluoride (536 mg,3.53 mmol). The solids were taken up in 10 mL ethanol, the flask wassealed, and the resulting mixture stirred at 60° C. After the reactionhad stirred for 18 hr. the mixture was filtered, diluted in 50 mL EtOAc,and washed with 20 mL each of 1 M aqueous sodium bicarbonate, saturatedammonium chloride, and brine. The remaining organics were dried overanhydrous sodium sulfate, filtered and concentrated in vacuo. A crudepurification was performed by filtration of the residue on silica gelplug (0→10% EtOAc/hexanes), yielding 320 mg of white solid thatcontained a mixture of the desired product and several small impurities.The resulting material was dissolved in a THF-ethanol mixture (4 mL,1:1), charged with 5% palladium on carbon (85 mg, 40 μmol), andhydrogenated at ambient pressure. After stirring for 4 hr. the blacksuspension was filtered and concentrated in vacuo. The residue wasrapidly dissolved in toluene (8 mL), degassed with argon for 2 min, thencharged with 2-methyl-3-buten-2-ol (250 μL, 2.4 mmol), and BF₃.OEt₂ (300μL, 2.4 mmol). The resulting brown solution was stirred at 100° C. After45 min, the reaction mixture was washed once with 1 M aqueous sodiumbicarbonate, dried over anhydrous sodium sulfate, filtered andconcentrated in vacuo. Purification by silica gel column chromatography(0→10% EtOAc/hexanes) afforded a yellow oil containing5-(4-fluorophenyl)-2,2,7,8-tetramethylchroman-6-ol and some impurities(250 mg). ¹H NMR (CDCl₃, 400 MHz) 7.3-7.1 (m, 41H), 4.25 (s, 1H), 2.28(t, 2H), 2.17 (s, 3H), 2.14 (s, 3H), 1.65 (t, 2H), 1.26 (s, 6H) ppm.

Step 32-(4-Fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

Purified residue containing5-(4-fluorophenyl)-2,2,7,8-tetramethylchroman-6-ol from the abovereaction (250 mg) was dissolved in acetonitrile (10 ml) and cooled in anice-water bath. To the resulting solution was added dropwise aqueoussolution of ceric ammonium nitrate (920 mg, 1.68 mmol in 10 mL) until areddish color persisted. When the titration endpoint was reached, themixture was diluted in 20 mL EtOAc, and washed once with brine (5 mL).The remaining organics were dried over anhydrous sodium sulfate,filtered and concentrated in vacuo. Purification by silica gel columnchromatography (5→25% EtOAc/hexanes) producing 80 mg of2-(4-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dion,a yellow oil. ¹H NMR (CDCl₃, 400 MHz) 7.09 (d, 4H), 2.40 (m, 2H), 2.07(s, 3H), 2.04 (s, 3H), 1.50 (m, 2H), 1.10 (s, 6H) ppm.

Similarly by substituting 4-fluorophenylboronic acid for other aryl orheterocyclyl boronic acids, the following compounds were produced.

Example 102-(3-Hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.58 (m, 3H), 7.12 (d, 2H), 2.39 (m, 2H), 2.07(s, 3H), 2.05 (s, 3H), 1.55 (m, 2H), 1.05 (s, 6H) ppm.

Example 112-(3-Hydroxy-3-methylbutyl)-5,6-dimethyl-3-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.67 (d, 2H), 7.25 (d, 2H), 2.38 (m, 2H), 2.08(s, 3H), 2.05 (s, 3H), 1.49 (m, 2H), 1.09 (s, 6H) ppm.

Example 122-(3-Hydroxy-3-methylbutyl)-3-(4-methoxyphenyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.05 (d, 2H), 6.93 (d, 2H), 2.42 (m, 2H), 2.05(s, 3H), 2.02 (s, 3H), 1.51 (m, 2H), 1.10 (s, 6H) ppm.

Example 132-(3-Hydroxy-3-methylbutyl)-5,6-dimethyl-3-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.88-7.80 (m, 3H), 7.62 (s, 1H), 7.52-7.47 (m,2H), 7.23-7.21 (m, 2H), 2.45 (m, 2H), 2.09 (s, 3H), 2.06 (s, 3H), 1.57(m, 2H), 1.04 (s, 6H) ppm.

Example 142-(Benzofuran-2-yl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.65 (d, 1H), 7.47 (d, 1H), 7.37 (s, 1H),7.35-7.24 (m, 3H), 2.91 (m, 2H), 2.08 (s, 6H), 1.75 (m, 2H), 1.29 (s,6H) ppm.

Example 152-(4-Chlorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.85 (d, 2H), 7.06 (d, 2H), 2.39 (m, 2H), 2.06(s, 3H), 2.04 (s, 3H), 1.49 (m, 2H), 1.10 (s, 6H) ppm.

Example 162-(4-Ethylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.22 (d, 2H), 7.02 (d, 2H), 2.65 (q, 2H), 2.40(m, 2H), 2.06 (s, 3H), 2.03 (s, 3H), 1.51 (m, 2H), 1.23 (t, 3H), 1.08(s, 6H) ppm.

Example 172-(3-Hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.66 (d, 1H), 7.54 (t, 1H), 7.40 (s, 1H), 7.32(d, 1H), 2.37 (m, 2H), 2.07 (s, 3H), 2.05 (s, 3H), 1.51 (m, 2H), 1.08(s, 6H) ppm.

Example 182-(4-tert-Butylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.40 (d, 2H), 7.05 (d, 2H), 2.40 (m, 2H), 2.06(s, 3H), 2.03 (s, 3H), 1.50 (m, 2H), 1.06 (s, 6H) ppm.

Example 192-(3-Hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.70 (d, 2H), 7.23 (d, 2H), 2.37 (m, 2H), 2.07(s, 3H), 2.04 (s, 3H), 1.49 (m, 2H), 1.09 (s, 6H) ppm.

Example 202-(3-Fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.40 (m, 1H), 7.09 (m, 1H), 6.91-6.82 (m, 2H),2.38 (m, 2H), 2.07 (s, 3H), 2.04 (s, 3H), 1.51 (m, 2H), 1.09 (s, 6H)ppm.

Example 212-(3,4-Difluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.38 (m, 1H), 7.21-7.06 (m, 2H), 2.38 (m, 2H),2.07 (s, 3H), 2.05 (s, 3H), 1.48 (m, 2H), 1.07 (s, 3H), 1.06 (s, 3H)ppm.

Example 222-(2-Fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.37 (m, 1H), 7.19 (m, 1H), 7.10 (m 2H), 2.38(m, 2H), 2.07 (s, 3H), 2.05 (s, 3H), 1.48 (m, 2H), 1.07 (s, 3H), 1.05(s, 3H) ppm.

Example 232-Benzyl-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.26-7.22 (m, 3H), 7.18-7.14 (m, 2H), 3.87 (s,2H), 2.60 (m, 2H), 2.00 (s, 6H), 1.37 (m, 2H), 1.19 (s, 6H) ppm.

Example 242-(3-Hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-phenylpropyl)cyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz 7.28-7.24 (m, 3H), 7.19-7.17 (m, 2H), 2.69 (t,2H), 2.42 (m, 4H), 1.98 (m, 6H), 1.73 (m, 2H), 1.44 (m, 2H), 1.18 (s,6H) ppm.

Example 252-(3-Hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.29-7.23 (m, 3H), 7.20-7.18 (m, 2H), 2.73 (s,2H), 2.41 (m, 2H), 2.00 (m, 6H), 1.39 (m, 2H), 1.21 (s, 6H) ppm.

Example 262-(1-Hydroxy-2-phenylethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione

¹H NMR (CDCl₃, 400 MHz) 7.28-7.14 (m, 5H), 4.81 (m, 1H), 3.69 (d, 1H),2.38 (m, 1H), 2.19 (m, 1H), 2.02 (s, 3H), 2.00 (s, 3H), 1.32 (m, 1H),1.15 (s, 6H), 1.05 (m, 1H) ppm.

BIOLOGICAL EXAMPLES Example A Screening Compounds of the Invention inHuman Dermal Fibroblasts from Friedreich's Ataxia Patients

An initial screen was performed to identify compounds effective for theamelioration of redox disorders. Test samples, 4 reference compounds(Idebenone, decylubiquinone, Trolox and α-tocopherol acetate), andsolvent controls were tested for their ability to rescue FRDAfibroblasts stressed by addition of L-buthionine-(S,R)-sulfoximine(BSO), as described in Jauslin et al., Hum. Mol. Genet. 11(24):3055(2002), Jauslin et al., FASEB J. 17:1972-4 (2003), and InternationalPatent Application WO 2004/003565. Human dermal fibroblasts fromFriedreich's Ataxia patients have been shown to be hypersensitive toinhibition of the de novo synthesis of glutathione (GSH) withL-buthionine-(S,R)-sulfoximine (BSO), a specific inhibitor of GSHsynthetase (Jauslin et al., Hum. Mol. Genet. 11 (24):3055 (2002)). Thisspecific BSO-mediated cell death can be prevented by administration ofantioxidants or molecules involved in the antioxidant pathway, such asα-tocopherol, selenium, or small molecule glutathione peroxidasemimetics. However, antioxidants differ in their potency, i.e. theconcentration at which they are able to rescue BSO-stressed FRDAfibroblasts.

MEM (a medium enriched in amino acids and vitamins, catalog no.1-31F24-I) and Medium 199 (M 199, catalog no. 1-21F22-I) with Earle'sBalanced Salts, without phenol red, were purchased from Bioconcept.Fetal Calf Serum was obtained from PAA Laboratories. Basic fibroblastgrowth factor and epidermal growth factor were purchased from PeproTech.Penicillin-streptomycin-glutamine mix, L-buthionine (S,R)-sulfoximine,(+)-α-tocopherol acetate, decylubiquinone, and insulin from bovinepancreas were purchased from Sigma. Trolox(6-hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid) was obtainedfrom Fluka. Idebenone was obtained from Chemo Iberica. Calcein AM waspurchased from Molecular Probes. Cell culture medium was made bycombining 125 ml M 199 EBS, 50 ml Fetal Calf Serum, 100 U/ml penicillin,100 μg/ml streptomycin, 2 mM glutamine, 10 μg/ml insulin, 10 ng/ml EGF,and 10 ng/ml bFGF; MEM EBS was added to make the volume up to 500 ml. A10 mM BSO solution was prepared by dissolving 444 mg BSO in 200 ml ofmedium with subsequent filter-sterilization. During the course of theexperiments, this solution was stored at +4° C. The cells were obtainedfrom the Coriell Cell Repositories (Camden, N.J.; repository numberGM04078) and grown in 10 cm tissue culture plates. Every third day, theywere split at a 1:3 ratio.

The test samples were supplied in 1.5 ml glass vials. The compounds werediluted with DMSO, ethanol or PBS to result in a 5 mM stock solution.Once dissolved, they were stored at −20° C. Reference antioxidants(Idebenone, decylubiquinone, α-tocopherol acetate and trolox) weredissolved in DMSO.

Test samples were screened according to the following protocol: Aculture with FRDA fibroblasts was started from a 1 ml vial withapproximately 500,000 cells stored in liquid nitrogen. Cells werepropagated in 10 cm cell culture dishes by splitting every third day ina ratio of 1:3 until nine plates were available. Once confluent,fibroblasts were harvested. For 54 micro titer plates (96 well-MTP) atotal of 14.3 million cells (passage eight) were re-suspended in 480 mlmedium, corresponding to 100 μl medium with 3,000 cells/well. Theremaining cells were distributed in 10 cm cell culture plates (500,000cells/plate) for propagation. The plates were incubated overnight at 37°C. in a atmosphere with 95% humidity and 5% CO₂ to allow attachment ofthe cells to the culture plate.

MTP medium (243 μl) was added to a well of the microtiter plate. Thetest compounds were unfrozen, and 7.5 μl of a 5 mM stock solution wasdissolved in the well containing 243 μl medium, resulting in a 150 μMmaster solution. Serial dilutions from the master solution were made.The period between the single dilution steps was kept as short aspossible (generally less than 1 second).

Plates were kept overnight in the cell culture incubator. The next day,10 μl of a 10 mM BSO solution were added to the wells, resulting in a 1mM final BSO concentration. Forty-eight hours later, three plates wereexamined under a phase-contrast microscope to verify that the cells inthe 0% control (wells E1-H1) were clearly dead. The medium from allplates was discarded, and the remaining liquid was removed by gentlytapping the plate inversed onto a paper towel.

100 μl of PBS containing 1.2 μM Calcein AM were then added to each well.The plates were incubated for 50-70 minutes at room temperature. Afterthat time the PBS was discarded, the plate gently tapped on a papertowel and fluorescence (excitation/emission wavelengths of 485 nm and525 nm, respectively) was read on a Gemini fluorescence reader. Data wasimported into Microsoft Excel (EXCEL is a registered trademark ofMicrosoft Corporation for a spreadsheet program) and used to calculatethe EC₅₀ concentration for each compound.

The compounds were tested three times, i.e., the experiment wasperformed three times, the passage number of the cells increasing by onewith every repetition.

The solvents (DMSO, ethanol, PBS) neither had a detrimental effect onthe viability of non-BSO treated cells nor did they have a beneficialinfluence on BSO-treated fibroblasts even at the highest concentrationtested (1%). None of the compounds showed auto-fluorescence. Theviability of non-BSO treated fibroblasts was set as 100%, and theviability of the BSO- and compound-treated cells was calculated asrelative to this value.

The following table summarizes the EC₅₀ for the four control compounds.

EC₅₀ [μM] Compound Value 1 Value 2 Value 3 Average Stdev Decylubiquinone0.05 0.035 0.03 0.038 0.010 alpha-Tocopherol acetate 0.4 0.15 0.35 0.300.13 Idebenone 1.5 1 1 1.2 0.3 Trolox 9 9 8 8.7 0.6

Certain compounds of the present invention such as:

-   2-(3-hydroxy-3-methylhutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-6-(4-methoxyphenyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   4-(5-(3-hydroxy-3-methylbutyl)-2,4-dimethyl-3,6-dioxocyclohexa-1,4-dienyl)benzonitrile;-   2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(3,4-difluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-fluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;    and-   2-benzyl-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-phenylpropyl)cyclohexa-2,5-diene-1,4-dione;-   2-(1-hydroxy-2-phenylethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(4-(trifluoromethyl)-phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(4-chlorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-ethylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-(trifluoromethyl)phenyl)-cyclohexa-2,5-diene-1,4-dione;-   2-(4-tert-butylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(4-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3,4-difluorophenyl)-3-(3-hydroxy-3-methylhutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;    and-   2-(4-chlorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione.    exhibited protection against FRDA with an EC₅₀ of less than about    200 nM.

Example B Screening Compounds of the Invention in Fibroblasts fromHuntington's Patients

Compounds of the invention were tested using the screen as described inExample A, but substituting FRDA cells with Huntington's cells obtainedfrom the Coriell Cell Repositories (Camden, N.J.; repository number GM04281). The compounds were tested for their ability to rescue humandermal fibroblasts from Huntington's patients from oxidative stress.

Certain compounds of the present invention such as:

-   2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-6-(4-methoxyphenyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(3,4-difluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-fluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenethylcyclohexa-2,5-diene-1,4-dione;-   2-benzyl-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-phenylpropyl)cyclohexa-2,5-diene-1,4-dione;-   2-(1-hydroxy-2-phenylethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-3-(4-methoxyphenyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(4-(trifluoromethyl)-phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(4-chlorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-ethylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-(trifluoromethyl)phenyl)-cyclohexa-2,5-diene-1,4-dione;-   2-(4-tert-butylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(4-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   4-(2-(3-hydroxy-3-methylbutyl)-4,5-dimethyl-3,6-dioxocyclohexa-1,4-dienyl)benzonitrile;-   2-(3,4-difluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(2-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-3-(3-methoxyphenyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(4-fluoro-2-methoxyphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(benzo[d][1,3]dioxol-5-yl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;    exhibited protection against Huntington's with an EC₅₀ of less than    about 200 nM.

Example C Screening Compounds of the Invention in Fibroblasts fromLeber's Hereditary Optic Neuropathy Patients

Compounds of the invention were screened as described in Example A, butsubstituting FRDA cells with Leber's Hereditary Optic Neuropathy (LHON)cells obtained from the Coriell Cell Repositories (Camden, N.J.;repository number GM03858). The compounds were tested for their abilityto rescue human dermal fibroblasts from LHON patients from oxidativestress.

Certain compounds of the present invention such as:

-   2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-6-(4-methoxyphenyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   4-(5-(3-hydroxy-3-methylbutyl)-2,4-dimethyl-3,6-dioxocyclohexa-1,4-dienyl)benzonitrile;-   2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(3,4-difluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;    and-   2-(4-fluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenethylcyclohexa-2,5-diene-1,4-dione;-   2-benzyl-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-phenylpropyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-3-(4-methoxyphenyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(4-(trifluoromethyl)-phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(benzofuran-2-yl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-chlorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-ethylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-(trifluoromethyl)phenyl)-cyclohexa-2,5-diene-1,4-dione;-   2-(4-tert-butylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(4-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3,4-difluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;    and-   2-(4-chlorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione.    exhibited protection against LHON with an EC₅₀ of less than about    200 nM.

Example D Screening Compounds of the Invention in Fibroblasts fromParkinson's Disease Patients

Compounds of the invention were screened as described in Example A, butsubstituting FRDA cells with Parkinson's Disease (PD) cells obtainedfrom the Coriell Cell Repositories (Camden, N.J.; repository numberAG20439). The compounds were tested for their ability to rescue humandermal fibroblasts from Parkinson's disease patients from oxidativestress.

Certain compounds of the present invention such as:

-   2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-6-(4-methoxyphenyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   4-(5-(3-hydroxy-3-methylbutyl)-2,4-dimethyl-3,6-dioxocyclohexa-1,4-dienyl)benzonitrile;-   2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(3,4-difluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;    and-   2-(4-fluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-phenylpropyl)cyclohexa-2,5-diene-1,4-dione;-   2-(1-hydroxy-2-phenylethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(4-(trifluoromethyl)-phenyl)cyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;-   2-(benzofuran-2-yl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-chlorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(4-ethylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;-   2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-(trifluoromethyl)phenyl)-cyclohexa-2,5-diene-1,4-dione;-   2-(4-tert-butylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;-   2-(3-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;    exhibited protection against PD with an EC₅₀ of less than about 200    nM.

Example E Screening Compounds of the Invention in Fibroblasts from CoQ10Deficient Patients

Compounds of the invention are tested using a screen similar to the onedescribed in Example A, but substituting FRDA cells with cells obtainedfrom CoQ10 deficient patients harboring a CoQ2 mutation. The compoundswere tested for their ability to rescue human dermal fibroblasts fromCoQ10 deficient patients from oxidative stress. Compounds of the presentinvention are considered active if they exhibit protection against CoQ10deficiency with an EC₅₀ of less than about 200 nM

Example F Screening Compounds of the Invention in Human DermalFibroblasts from Autistic Patients

A screen is performed to identify compounds effective for theamelioration of ASD. Test samples, and solvent controls were tested fortheir ability to rescue Autistic Syndrome Disorder (ASD) fibroblastsstressed by addition of L-buthionine-(S,R)-sulfoximine (BSO).

MEM (a medium enriched in amino acids and vitamins, catalog no. Gibco11965) and Fetal Calf Serum are obtained from Invitrogen. Basicfibroblast growth factor and epidermal growth factor were purchased fromPeproTech. Penicillin-streptomycin-glutamine mix. L-buthionine(S,R)-sulfoximine, and insulin from bovine pancreas were purchased fromSigma. Calcein AM was purchased from Molecular Probes. Cell culturemedium (ATP) was made by combining 75 ml Fetal Calf Serum, 100 U/mlpenicillin, 100 μg/ml streptomycin, 2 mM glutamine, 10 ng/ml EGF, and 10ng/ml bFGF; MEM EBS is added to make the volume up to 500 ml. A 10 mMBSO solution was prepared by dissolving 444 mg BSO in 200 ml of mediumwith subsequent filter-sterilization. During the course of theexperiments, this solution was stored at +4° C. The cells obtained fromDr. J. M. Shoffner, Medical Neurogenetics, Atlanta, Ga. were grown in 10cm tissue culture plates. Every week, they were split at a 1:3 ratio.

The samples were supplied in 1.5 ml glass vials. The compounds werediluted with DMSO, ethanol or PBS to result in a 5 mM stock solution.Once dissolved, they were stored at −20° C.

The samples are screened according to the following protocol: A culturewith ASD fibroblasts was started from a 1 ml vial with approximately500,000 cells stored in liquid nitrogen. Cells were propagated in 10 cmcell culture dishes by splitting every week in a ratio of 1:3 until nineplates are available. Once confluent, fibroblasts were harvested. For 54micro titer plates (96 well-MTP) a total of 14.3 million cells (passageeight) were re-suspended in 480 ml medium, corresponding to 100 μlmedium with 3,000 cells/well. The remaining cells were distributed in 10cm cell culture plates (500,000 cells/plate) for propagation. The plateswere incubated overnight at 37° C. in an atmosphere with 95% humidityand 5% CO₂ to allow attachment of the cells to the culture plate.

MTP medium (243 μl) was added to a well of the microtiter plate. Thetest compounds are unfrozen, and 7.5 μl of a 5 mM stock solution wasdissolved in the well containing 243 μl medium, resulting in a 150 μMmaster solution. Serial dilutions from the master solution were made.The period between the single dilution steps was kept as short aspossible (generally less than 1 second).

Plates were kept overnight in the cell culture incubator. The next day,10 μl of a 10 mM BSO solution were added to the wells, resulting in a 1mM final BSO concentration. Forty-eight hours later, three plates wereexamined under a phase-contrast microscope to verify that the cells inthe 0% control (wells E1-H1) were clearly dead. The medium from allplates was discarded, and the remaining liquid was removed by gentlytapping the plate inversed onto a paper towel.

100 μl of PBS containing 1.2 μM Calcein AM were then added to each well.The plates were incubated for 50-70 minutes at room temperature. Afterthat time the PBS was discarded, the plate gently tapped on a papertowel and fluorescence (excitation/emission wavelengths of 485 nm and525 nm, respectively) was read on a Gemini fluorescence reader. Data wasimported into Microsoft Excel® and used to calculate the EC₅₀concentration for each compound.

The compounds were tested three times, i.e., the experiment wasperformed three times, the passage number of the cells increasing by onewith every repetition.

The solvents (DMSO, ethanol, PBS) neither had a detrimental effect onthe viability of non-BSO treated cells nor do they had a beneficialinfluence on BSO-treated fibroblasts even at the highest concentrationtested (1%). None of the compounds showed auto-fluorescence. Theviability of non-BSO treated fibroblasts was set as 100%, and theviability of the BSO- and compound-treated cells was calculated asrelative to this value.

Certain compounds of the present invention were considered to be activeif they exhibited protection against ASD with an EC₅₀ of less than 300nM.

The disclosures of all publications, patents, patent applications andpublished patent applications referred to herein by an identifyingcitation are hereby incorporated herein by reference in their entirety.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it is apparent to those skilled in the art that certainminor changes and modifications will be practiced. Therefore, thedescription and examples should not be construed as limiting the scopeof the invention.

1. A method of treating or suppressing a mitochondrial disorder,modulating one or more energy biomarkers, normalizing one or more energybiomarkers, or enhancing one or more energy biomarkers, comprisingadministering to a subject a therapeutically effective amount oreffective amount of one or more compounds of Formula I:

where, R is selected from the group consisting of:

where the * indicates the point of attachment of R to the remainder ofthe molecule; where M and M′ are independently selected from the groupconsisting of hydrogen, —C(O)—R′, —C(O)—(C₂-C₆)-alkenyl,—C(O)—(C₂-C₆)-alkynyl, —C(O)-aryl, —C(O)-heterocyclyl, —C(O)O—R′,—C(O)NR′R″, —SO₂OR′, —SO₂—(C₁-C₆)-alkyl, —SO₂—(C₁-C₆)-haloalkyl,—SO₂-aryl, —SO₂—NR′R″, —P(O)(OR′)(OR″), and C-linked mono or di-peptide,where R′ and R″ are each independently of each other hydrogen or(C₁-C₆)-alkyl optionally substituted with —OH, —NH₂, —NH(C₁-C₄)alkyl,—N((C₁-C₄)alkyl)₂, —C(O)—OH, —C(O)—O—(C₁-C₄)-alkyl or halogen; whereeither R¹ is aryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-, whereinthe aryl or heterocyclyl is optionally substituted with one or moresubstituents selected from the group consisting of (C₁-C₆)-alkyl,(C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl, hydroxy,(C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, thiol,(C₁-C₆)-thioalkyl, and —COR⁴; and wherein the (C₀-C₆)-alkyl group isoptionally substituted with OH, —O(C₁-C₄)-alkyl, —NH₂, —NH(C₁-C₄)-alkyl,—N((C₁-C₄)-alkyl)₂, oxo or halogen; and R² and R³ are independentlyselected from the group consisting of hydrogen, halogen, (C₁-C₆)-alkyland (C₁-C₆)-alkoxy, or R³ is aryl-(C₀-C₆)-alkyl- orheterocyclyl-(C₀-C₆)-alkyl-, wherein the aryl or heterocyclyl isoptionally substituted with one or more substituents selected from thegroup consisting of (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl,halogen, (C₁-C₆)-haloalkyl-, hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴,—NR⁵R⁶, —CONR⁵R⁶, thiol, (C₁-C₆)-thioalkyl-, and —COR⁴; and wherein the(C₀-C₆)-alkyl group is optionally substituted with OH, —O(C₁-C₄)-alkyl,—NH₂, —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂, oxo or halogen; and R¹ andR² are independently selected from the group consisting of hydrogen,halogen, (C₁-C₆)-alkyl, and (C₁-C₆)-alkoxy; where R⁴ is hydrogen,(C₁-C₆)-alkyl, aryl, or aryl-(C₁-C₆)-alkyl-; and where R⁵ and R⁶ areindependently of each other hydroxy, (C₁-C₆)-alkoxy, (C₁-C₆)-alkyl,(C₂-C₆)-alkenyl, (C₂-C₆)-alkynyl, aryl, aryl-(C₁-C₆)-alkyl-,heterocyclyl, or heterocyclyl-(C₁-C₆)-alkyl-; wherein the alkyl,alkenyl, alkynyl, aryl and heterocyclyl groups are optionally furthersubstituted with oxo, halogen, (C₁-C₆)-haloalkyl, hydroxy,(C₁-C₆)-alkoxy, or —COOR⁴; or a salt, a stereoisomer, or a mixture ofstereoisomers thereof and additionally optionally comprising apharmaceutically acceptable excipient.
 2. The method of claim 1 wherethe method is a method of treating a mitochondrial disorder, modulatingone or more energy biomarkers, normalizing one or more energybiomarkers, or enhancing one or more energy biomarkers, comprisingadministering to a subject a therapeutically effective amount oreffective amount of the one or more compounds of Formula I. 3.(canceled)
 4. The method according to claim 1 wherein R, in the one ormore compounds, is

or a salt, a stereoisomer, or a mixture of stereoisomers thereof.
 5. Themethod of claim 4 where, in the one or more compounds, R¹ isaryl-(C₀-C₆)-alkyl- or heterocyclyl-(C₀-C₆)-alkyl-, wherein the aryl orheterocyclyl is optionally substituted with one or more substituentsselected from the group consisting of (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl,(C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl, hydroxy, (C₁-C₆)-alkoxy,CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, thiol, (C₁-C₆)-thioalkyl, and—COR⁴; and wherein the (C₀-C₆)-alkyl group is optionally substitutedwith OH, —O(C₁-C₄)-alkyl, —NH₂, —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂ oxoor halogen; and R² and R³ are independently selected from the groupconsisting of hydrogen, halogen, (C₁-C₆)-alkyl, and (C₁-C₆)-alkoxy; or asalt, a stereoisomer, or a mixture of stereoisomers thereof.
 6. Themethod of claim 5 where, in the one or more compounds, R² and R³ are(C₁-C₆)-alkyl; or a salt, a stereoisomer, or a mixture of stereoisomersthereof.
 7. The method of claim 5 where, in the one or more compounds,R¹ is aryl-(C₀-C₆)-alkyl-, wherein the aryl is optionally substitutedwith one or more substituents selected from the group consisting of(C₁-C₆)-alkyl, halogen, (C₁-C₆)-haloalkyl, hydroxy, (C₁-C₆)-alkoxy, CN,—COOR⁴, and —COR⁴; or a salt, a stereoisomer, or a mixture ofstereoisomers thereof. 8-10. (canceled)
 11. The method of claim 5 where,in the one or more compounds, R¹ is heterocyclyl-(C₀-C₆)-alkyl-, whereinthe heterocyclyl is optionally substituted with one or more substituentsindependently selected from the group consisting of (C₁-C₆)-alkyl,halogen, (C₁-C₆)-haloalkyl, hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴,—NR⁵R⁶, —CONR⁵R⁶, and —COR⁴; or a salt, a stereoisomer, or a mixture ofstereoisomers thereof. 12-22. (canceled)
 23. The method of claim 4where, in the one or more compounds, R¹ and R² are independentlyselected from the group consisting of hydrogen, halogen, (C₁-C₆)-alkyland (C₁-C₆)-alkoxy; and R³ is aryl-(C₀-C₆)-alkyl- orheterocyclyl-(C₀-C₆)-alkyl-, wherein the aryl or heterocyclyl- isoptionally substituted with one or more substituents independentlyselected from the group consisting of (C₁-C₆)-alkyl, (C₂-C₆)-alkenyl,(C₂-C₆)-alkynyl, halogen, (C₁-C₆)-haloalkyl-, hydroxy, (C₁-C₆)-alkoxy,CN, nitro, —COOR⁴, —NR⁵R⁶, —CONR⁵R⁶, thiol, (C₁-C₆)-thioalkyl-, and—COR⁴; and wherein the (C₀-C₆)-alkyl group is optionally substitutedwith OH, —O(C₁-C₄)-alkyl, —NH₂, —NH(C₁-C₄)-alkyl, —N((C₁-C₄)-alkyl)₂,oxo or halogen; or a salt, a stereoisomer, or a mixture of stereoisomersthereof.
 24. The method of claim 23 where, in the one or more compounds,R¹ and R² are (C₁-C₆)-alkyl; or a salt, a stereoisomer, or a mixture ofstereoisomers thereof.
 25. The method of claim 23 where, in the one ormore compounds, R³ is aryl-(C₀-C₆)-alkyl-, wherein the aryl isoptionally substituted with one or more substituents independentlyselected from the group consisting of (C₁-C₆)-alkyl, halogen,(C₁-C₆)-haloalkyl, hydroxy, (C₁-C₆)-alkoxy, CN, —COOR⁴, and —COR⁴; or asalt, a stereoisomer, or a mixture of stereoisomers thereof. 26-28.(canceled)
 29. The method of claim 23 where, in the one or morecompounds, R³ is heterocyclyl-(C₀-C₆)-alkyl-, wherein the heterocyclylis optionally substituted with one or more substituents independentlyselected from the group consisting of (C₁-C₆)-alkyl, halogen,(C₁-C₆)-haloalkyl, hydroxy, (C₁-C₆)-alkoxy, CN, nitro, —COOR⁴, —NR⁵R⁶,—CONR⁵R⁶, and —COR⁴; or a salt, a stereoisomer, or a mixture ofstereoisomers thereof. 30-51. (canceled)
 52. The method according toclaim 5 where, in the one or more compounds, R¹ is phenylmono-substituted with a substituent selected from the group consistingof fluoro, chloro, and trifluoromethyl.
 53. The method according toclaim 23 where, in the one or more compounds, R³ is phenylmono-substituted with a substituent selected from the group consistingof fluoro, chloro, and trifluoromethyl.
 54. The method according toclaim 1 wherein the one or more compounds are selected from the groupconsisting of:2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-6-(4-methoxyphenyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;4-(5-(3-hydroxy-3-methylbutyl)-2,4-dimethyl-3,6-dioxocyclohexa-1,4-dienyl)benzonitrile;2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;2-(3,4-difluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;2-(4-fluorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;2-(4-chlorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;2-(2,3-dihydrobenzofuran-2-yl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenethylcyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-phenylcyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-phenylpropyl)cyclohexa-2,5-diene-1,4-dione;2-(1-hydroxy-2-phenylethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-3-(4-methoxyphenyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(4-(trifluoromethyl)-phenyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(naphthalen-2-yl)cyclohexa-2,5-diene-1,4-dione;2-(benzofuran-2-yl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(4-chlorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(4-ethylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(3-(trifluoromethyl)phenyl)-cyclohexa-2,5-diene-1,4-dione;2-(4-tert-butylphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;2-(4-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(3-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;4-(2-(3-hydroxy-3-methylbutyl)-4,5-dimethyl-3,6-dioxocyclohexa-1,4-dienyl)benzonitrile;2-(3,4-difluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;2-(2-fluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-3-(3-methoxyphenyl)-5,6-dimethyl-cyclohexa-2,5-diene-1,4-dione;2-(4-fluoro-2-methoxyphenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(benzo[d][1,3]dioxo1-5-yl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(2,4-difluorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(3,5-bis(trifluoromethyl)phenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(thiazol-2-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(thiazol-5-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(pyridin-2-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(pyridazin-4-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(thiophen-2-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(thiophen-3-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;2-(2-(furan-2-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(2-(furan-3-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(2-(1H-pyrazol-5-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(2-(1H-pyrazol-4-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(2-(1H-pyrazol-1-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(2-(1H-imidazol-5-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(2-(1H-imidazol-2-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(oxazol-5-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(oxazol-2-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(2-(oxazol-4-yl)ethyl)cyclohexa-2,5-diene-1,4-dione;and2-(2-(1H-indol-3-yl)ethyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;or a salt, stereoisomer, or mixture of stereoisomers thereof.
 55. Themethod according to claim 1, wherein the one or more compounds areselected from the group consisting of:2-(3-hydroxy-3-methylbutyl)-3,5-dimethyl-6-(4-(trifluoromethyl)phenyl)cyclohexa-2,5-diene-1,4-dione;2-(3-hydroxy-3-methylbutyl)-5,6-dimethyl-3-(4-(trifluoromethyl)-phenyl)cyclohexa-2,5-diene-1,4-dione;2-(4-chlorophenyl)-3-(3-hydroxy-3-methylbutyl)-5,6-dimethylcyclohexa-2,5-diene-1,4-dione;and2-(4-chlorophenyl)-6-(3-hydroxy-3-methylbutyl)-3,5-dimethylcyclohexa-2,5-diene-1,4-dione;and or a salt thereof.
 56. The method of claim 1, where the method is amethod of treating or suppressing a mitochondrial disorder, wherein themitochondrial disorder is selected from the group consisting of aninherited mitochondrial disease; Myoclonic Epilepsy with Ragged RedFibers (MERRF); Mitochondrial Myopathy; Encephalopathy; Lactacidosis;Stroke (MELAS); Leber's Hereditary Optic Neuropathy (LHON); chronicprogressive external ophthalmoplegia (CPEO); Leigh Disease; Kearns-SayreSyndrome (KSS); Friedreich's Ataxia (FA); Co-Enzyme Q10 Deficiency;Complex I Deficiency, Complex II Deficiency; Complex III Deficiency;Complex IV Deficiency, Complex V Deficiency, Parkinson's disease;Alzheimer's disease; amyotrophic lateral sclerosis (ALS); musculardystrophy, Huntington's disease; a pervasive developmental disorder,epilepsy; macular degeneration; diabetes; cancer; a cerebral vascularaccident; autism; myopathy; cardiomyopathy; renal tubular acidosis;neurodegenerative diseases; motor neuron diseases; other neurologicaldiseases; genetic diseases; mood disorders; schizophrenia; bipolardisorder, age-associated diseases; cerebral vascular diseases; autisticdisorder (ASD); Asperger's disorder, childhood disintegrative disorder(CDD); Rett's disorder, PDD-Not Otherwise Specified (PDD-NOS);Mitochondrial encephalomyopathy, lactic acidosis, and stroke-likeepisodes (MELAS); neuronal injury associated with seizures; and neuronalinjury associated with ischemia.
 57. The method of claim 4, where themethod is a method of treating or suppressing a mitochondrial disorder,wherein the mitochondrial disorder is selected from the group consistingof an inherited mitochondrial disease; Myoclonic Epilepsy with RaggedRed Fibers (MERRF); Mitochondrial Myopathy; Encephalopathy;Lactacidosis; Stroke (MELAS); Leber's Hereditary Optic Neuropathy(LHON); chronic progressive external ophthalmoplegia (CPEO); LeighDisease; Kearns-Sayre Syndrome (KSS); Friedreich's Ataxia (FA);Co-Enzyme Q10 Deficiency; Complex I Deficiency, Complex II Deficiency;Complex III Deficiency; Complex IV Deficiency, Complex V Deficiency,Parkinson's disease; Alzheimer's disease; amyotrophic lateral sclerosis(ALS); muscular dystrophy, Huntington's disease; a pervasivedevelopmental disorder, epilepsy; macular degeneration; diabetes;cancer; and a cerebral vascular accident; autism; myopathy;cardiomyopathy; renal tubular acidosis; neurodegenerative diseases;motor neuron diseases; other neurological diseases; genetic diseases;mood disorders; schizophrenia; bipolar disorder, age-associateddiseases; cerebral vascular diseases; autistic disorder (ASD);Asperger's disorder, childhood disintegrative disorder (CDD); Rett'sdisorder; PDD-Not Otherwise Specified (PDD-NOS); Mitochondrialencephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS);neuronal injury associated with seizures; and neuronal injury associatedwith ischemia.
 58. The method of claim 56, wherein the method is amethod of treating the mitochondrial disorder, wherein the mitochondrialdisorder is selected from the group consisting of Parkinson's disease;Alzheimer's disease; Huntington's disease; epilepsy; amyotrophic lateralsclerosis (ALS); and macular degeneration.
 59. The method of claim 1,wherein the method is a method of modulating, normalizing, or enhancingone or more energy biomarkers, where the one or more energy biomarkersare selected from the group consisting of: lactic acid (lactate) levels,either in whole blood, plasma, cerebrospinal fluid, or cerebralventricular fluid; pyruvic acid (pyruvate) levels, either in wholeblood, plasma, cerebrospinal fluid, or cerebral ventricular fluid;lactate/pyruvate ratios, either in whole blood, plasma, cerebrospinalfluid, or cerebral ventricular fluid; phosphocreatine levels, NADH(NADH+H⁺) levels; NADPH (NADPH+H⁺) levels; NAD levels; NADP levels; ATPlevels; reduced coenzyme Q (CoQ^(red)) levels; oxidized coenzyme Q(CoQ^(ox′)) levels; total coenzyme Q (CoQ^(tot)) levels; oxidizedcytochrome C levels; reduced cytochrome C levels; oxidized cytochromeC/reduced cytochrome C ratio; acetoacetate levels, β-hydroxy butyratelevels, acetoacetate/β-hydroxy butyrate ratio,8-hydroxy-2′-deoxyguanosine (8-OHdG) levels; levels of reactive oxygenspecies; levels of oxygen consumption (VO2); levels of carbon dioxideoutput (VCO2); respiratory quotient (VCO2/VO2); exercise tolerance; andanaerobic threshold.